title: Genomic DNA from whole blood sample [SUAZ_013_meth_v1]

source_name: PESA study participant SUAZ_013_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_009_meth_v1]

status: Public on Jun 21 2023

type: genomic

city: Madrid

first: Juan

middle: Carlos

last: Silla-Castro

address: Melchor Fernandez Almagro 3

department: Bioinformatics

country: Spain

institute: CNIC

hyb_protocol: Converted DNAs were processed to be hybridised in the Infinium MethylationEPIC BeadChip BeadChip following the manufacturer's protocols (Illumina).

scan_protocol: Arrays were scanned using iScan System (Illumina).

data_processing:
Array intensities were extracted from idat files, filtered and normalized using the rnb.run.analysis function from Bioconductor package RnBeads version 2.0.1. Probes with SNPs overlap were removed and the greedy cut algorithm implemented in RnBeads was applied with a detection p-value > 0.05 for probe detection assessment. Normalized by the dasen method  generating M-Values  downstream analysis.
matrix processed value definition: Values after dasen normalization
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: bisulfite converted

molecule: genomic DNA

organism: Homo sapiens

source_name: PESA study participant SUAZ_009_meth_v1

label_protocol: DNA was bisulfite converted using EZ DNA Methylation Kits (Zymo Research) following manufacturer's recommendation.

growth_protocol: Blood samples were collected in S-Monovette EDTA K3 tubes (Sarstedt). 600 µl of blood were aliquoted in 0.75 ml 2D Barcoded Storage Tubes (Thermo Scientific) and stored at -80°C until processed.

extract_protocol: Blood samples were thawed quickly in a 37°C water bath for 2 min to avoid degradation. Samples were then processed using the QIAsymphony DNA Mini Kit for the QiAsymphony SP automated station (QiAgen), following the manufacturer´s instructions. Briefly, blood samples were lysed and incubated with magnetic beads for DNA purification. After a wash, DNA was eluted in 200 µl of elution buffer, and DNA concentration and quality were measured by QuBit (Invitrogen) and Nanoquant (Tecan), respectively.

tag: gender

value: Female

tag: age

tag: pesa score

value: Generalized


title: Genomic DNA from whole blood sample [SUAZ_008_meth_v1]

source_name: PESA study participant SUAZ_008_meth_v1

value: No


title: Genomic DNA from whole blood sample [SUAZ_007_meth_v1]

source_name: PESA study participant SUAZ_007_meth_v1

value: Male


title: Day 10 + Diff. Medium rep3

type: SRA

city: Nantes

first: Benjamin

last: Ory

address: 1 rue Gaston Veil

country: France

description:
D10.+.diff_rep3
39_3931Nantes_s24_CD14-J10plus_C_RNASeq_hs_i10

library_source: transcriptomic

data_processing:
RNA-Seq: FASTP was used for adpater trimming and to remove low-quality reads (Q>30). Reads were mapped to human genome (hg19) using HISAT2 (v. 2.1.0) and read quantification was performed using stringtie (v. 2.1.1).
ChIP-Seq: reads were aligned to human genome (hg19) using bwa mem (v. 0.7.17). Low quality reads (-q 20), PCR duplicates and non-uniquely aligned reads using samtools (v. 1.9). Inorder to remove repliacte specific signals (alignement files of replicates from the same donor were merged into one alignement file using samtools merge. Peak calling was then performed on the merged alignement files using recommendations from github page of MACS2 (https://github.com/taoliu/MACS/wiki/Advanced\%3A-Call-peaks-using-MACS2-subcommands). Using the recommandations, ChIP and input tracks were built separately and then broad peak calling was perfomed using q-value threshold of 1e-5. ROSE2 was used to identify super-enhancers among peaks outside of promoters (TSS +/-2500 b.p.).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files per sample include coverage, TPM, FPKM values for each gene.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: comma-delimited text files per sample include all enhancers and super-enhancers identified, as output from ROSE2

molecule: total RNA

source_name: Day 10 + Diff. Medium_PBMC

extract_protocol:
RNA-Seq: Cells were harvested, frozen and sent to Active Motif Inc. platform for library preparation and sequencing. Illumina TruSeq Stranded mRNA Sample Preparation Kit was used for library preparation.
ChIP-Seq: Cells were harvested, frozen and sent to Broad Institute’s Genomics Services platform for the ChIP data and to Active Motif Inc. platform for the input data. H3K27ac antibodies (Acetyl-Histone H3 K27 (D5E4) XR Rabbit mAB, Cell Signaling Technologies were used for precipitation. Library preparation and Sequencing for the ChIP-data were performed in a multiplexed system on a 96-well plate.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: healthy donor

tag: tissue

value: PBMC

tag: cell type

value: CD14+ pre-monocytes

tag: treatment

value: Day 10 + Diff. Medium


title: Genomic DNA from whole blood sample [SUAZ_014_meth_v1]

source_name: PESA study participant SUAZ_014_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_016_meth_v1]

source_name: PESA study participant SUAZ_016_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_005_meth_v1]

source_name: PESA study participant SUAZ_005_meth_v1

value: Intermediate


title: Day 10 + Diff. Medium rep2

description:
d10.+.diff_rep2
38_3931Nantes_s23_CD14-J10plus_B_RNASeq_hs_i9


title: Tag8G5_Tag01

city: Munich

first: Peter

last: Androvic

state: Bavaria

address: Feodor-Lynen-Strasse 17

country: Germany

institute: LMU Hospital, Institute for Stroke and Dementia Research

library_source: transcriptomic single cell

data_processing:
Fastq files were quality-controlled with FastQC and reads were then aligned using rnaSTAR to the GRCm38 (mm10) genome with addition of ERCC spike-in sequences. To obtain single cell gene expression matrices reads were counted with rnaSTAR using parameter “quantMode GeneCounts” and unstranded argument.
Assembly: mm10
Supplementary files format and content: Tab-separated counts per cell and cell metadata

organism: Mus musculus

extract_protocol:
18 days after LPC injection, mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; gray matter was isolated from the frontal cortex and white matter was isolated form optic tract, medial lemniscus and corpus callosum (attached gray matter and choroid plexus were carefully removed). Single cells were isolated using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D to a final concentration of 45 mM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. The dissociated cell suspension was passed through a 70 mm cell strainer before labeling. Subsequently, cells were blocked with mouse FcR-blocking reagent (CD16/CD32 Monoclonal Antibody) and then stained for with the antibodiy against CD11b (PE/Cy7,M1/70, eBioscience, Cat:48-0451-82,1:200) and afterwards washed with PBS (Sigma, D8537). Cells were then stained with DAPI (4’,6-diamidino-2-phenylindole, 1:10000 dilution; Sigma)  and viable (DAPI-negative) single CD11b-positive cells were sorted by flow cytometry (SH800; Sony) into 96 well plates filled with 4 mL lysis buffer containing 0.05% Triton X-100 (Sigma) and, ERCC spike-in Mix (1:24000000 dilution), 2.5 mM oligo-dT, 2.5 mM dNTP and 2 U/mL of recombinant RNase inhibitor (Clontech).
The 96-well plates containing the sorted single cells were thawed and incubated for 3 min at 72°C and thereafter immediately placed on ice. To perform reverse transcription (RT) we added into each well a master mix of 0.59 μL H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μL Recombinant RNase Inhibitor (Clontech), 2 μL Betaine (5 M Sigma), 0.5 μL DTT (100 mM) 0.06 μL MgCl2 (1 M Sigma), 0.1 μL Templateswitching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next RT reactions were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; ending with 70°C for 5 min for enzyme inactivation. Preamplification of cDNA was performed by adding 12.5 μL KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μL H2O, 0.25 μL ISPCR primers (10 μM, 5’ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μL Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 23 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure beads (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Libraries were assessed by Bio-analyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and quantified using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies). Further selection of samples was performed via qPCR assay against ubiquitin transcripts Ubb77 (primer 1 5’-GGAGAGTCCATCGTGGTTATTT-3’ primer 2 5’-ACCTCTAGGGTGATGGTCTT-3’, probe 5’-/5Cy5/TGCAGATCTTCGTGAAGACCTGAC/3IAbRQSp/-3’) measured on a LightCycler 480 Instrument II (Roche). Samples were normalized to 160 pg/μL. Sequencing libraries were constructed by using in-house produced Tn5 transposase. Libraries were barcoded, pooled and purified in 3 rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library. Libraries were then sequenced with 100 bp paired-end sequencing on DNBSeq platform (BGI group).

treatment_protocol: Lysophosphatidylcholine (LPC) injections were administered at the age of 16-18 weeks. A solution of 1% LPC (L4129, Sigma) in PBS was mixed with Monastral blue (274011, SigmaAldrich) at a concentration of 0.03% to aid with visualization of the lesion during tissue processing. Mice were anaesthetized with an intraperitoneal injection of MMF solution (0.5 mg medetomidin/kg (body weight), 5.0 mg midazolam/kg (body weight) and 0.05 mg fentanyl/kg (body weight)). Then, head fur was removed, the eyes were treated with bepanthene cream (1578847, Bayer) and a small incision in the skin was performed to expose the skull. The mouse was positioned into a stereotactic injection apparatus and a small hole was drilled at the following injection coordinates (from bregma): X, ± 1.0 mm; Y, −0.1 mm). A glass capillary containing the LPC–monastral blue solution was then lowered to Z: −1.30 mm from bregma, and 1 µL was injected at a rate of 100 nL/minute. Two minutes after the delivery of LPC, the capillary was slowly retracted. The mouse was then injected with 0.05 mg buprenorphin/kg (body weight), and the skin was sutured. Anesthesia was terminated by a subcutaneous injection of AFN solution, containing 2.5 mg/kg (body weight) atipamezol, 1.2 mg/kg (body weight) naloxon and 0.5 mg/kg (body weight) flumazenil.

value: CD11b+ cells

tag: strain


title: Genomic DNA from whole blood sample [SUAZ_020_meth_v1]

source_name: PESA study participant SUAZ_020_meth_v1

value: Focal


title: Genomic DNA from whole blood sample [SUAZ_001_meth_v1]

source_name: PESA study participant SUAZ_001_meth_v1


title: Day 10 + Diff. medium rep1

description:
d10.+.diff_rep1
37_3931Nantes_s22_CD14-J10plus_A_RNASeq_hs_i8

source_name: Day 10 + Diff. medium_PBMC

value: Day 10 + Diff. medium


title: Tag8G4_Tag01


title: Genomic DNA from whole blood sample [SUAZ_017_meth_v1]

source_name: PESA study participant SUAZ_017_meth_v1


title: Tag8G3_Tag01


title: Day 7 - Diff. Medium rep3

description:
d7.-.diff_rep3
30_3931Nantes_s15_CD14-J7minus_C_RNASeq_hs_i1

source_name: Day 7 - Diff. Medium_PBMC

value: Day 7 - Diff. Medium


title: Day 7 - Diff. Medium rep2

description:
d7.-.diff_rep2
29_3931Nantes_s14_CD14-J7minus_B_RNASeq_hs_i27


title: H292 CASP4 overexpressiong, rep3

city: Kitakyushu, Fukuoka

first: Yosuke

last: Chiba

address: 1-1 Iseigaoka, Yahatanishi-ku

country: Japan

institute: University of Occupational and Environmental Health

data_processing:
WinSCP software
we check the quality of the sequence data by fastQC and trim the fastq file by Trimmomatic.
Trimmed sequence reads were mapped to GRCH38/hg38 using bowtie2 version 2.2.6 and Tophat2 version 2.1.0
Read count extraction and normalization were performed using Cufflinks version 2.2.1.
Assembly: GRCH38/hg38
Assembly: Supplementary files format and content: Excel files include FPKM values for each Sample

growth_protocol: NCI-H292 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). At least 7.5 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA Library.

tag: cell line

value: Carcinoma; Mucoepidermoid Pulmonary

tag: genotype

value: Caspase-4 overexpressing


title: H292 Caspase-4 Knockout, rep1

value: Caspase-4 knockout


title: Tag8G8_Tag01


title: H292 CASP4 overexpressiong, rep2


title: H292 Caspase-4 Knockout, rep2


title: Tag8G2_Tag01


title: Genomic DNA from whole blood sample [SUAZ_006_meth_v1]

source_name: PESA study participant SUAZ_006_meth_v1


title: H292 Caspase-4 Knockout, rep3


title: Tag8G7_Tag01


title: H292 CASP4 overexpressiong, rep1


title: Day 7 - Diff. Medium rep1

description:
d7.-.diff_rep1
28_3931Nantes_s11_CD14-J7minus_A_RNASeq_hs_i25


title: H292 mock, rep3

value: mock


title: Tag8G1_Tag01


title: Tag8F7_Tag01


title: Day 7 + Diff. Medium rep2

description:
d7.+.diff_rep2
32_3931Nantes_s17_CD14-J7plus_B_RNASeq_hs_i3

source_name: Day 7 + Diff. Medium_PBMC

value: Day 7 + Diff. Medium


title: H292 mock, rep1


title: H292 mock, rep2


title: Day 7 + Diff. Medium rep3

description:
D7.+.diff_rep3
33_3931Nantes_s18_CD14-J7plus_C_RNASeq_hs_i4


title: Tag8F6_Tag01


title: human efferent duct tissue, scRNAseq

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Road

department: Genetics

country: USA

institute: Case Western Reserve University

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger v3.1.0
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: human efferent duct tissue

growth_protocol: Normal (i.e. no tumor invasion) epididymis tissue was collected within ~ 2 hr of orchiectomy surgery from patients with a clinical diagnosis of testicular cancer.  Caput tissue was cut into 1-2 mm pieces and digested with collagenase as detailed below. Human epididymis epithelial cells were grown on Primaria plastic (Corning) in CMRL-1066 media (containing 15% fetal calf serum, 2 mmol/L L-glutamine, 1 μg/mL hydrocortisone, 0.2 U/mL insulin, and 10−10 mol/L cholera toxin) as described in DOI: 10.1016/j.fertnstert.2014.11.022

extract_protocol:
Normal (i.e. no tumor invasion) epididymis tissue was collected within ~ 2 hr of orchiectomy surgery from patients with a clinical diagnosis of testicular cancer.  Efferent duct and caput tissue was cut into 1-2 mm pieces and digested with collagenase (2 mg/mL collagenase + 40 U/mL DNAse I, Worthington Biochemical Corp.) at 37°C for 2 hr with constant shaking. Digesting tissue was then agitated by pipetting, allowed to settle for 4 min and the supernatant collected and stored on ice as cell suspension 1. Fresh collagenase solution was then added to the tissue, which was digested for a further 2 hr with shaking at 37°C, with subsequent agitation and settling as before. The supernatant (cell suspension 2) was then pooled with cell suspension 1 and tissue debris removed by passage through a 100-µm cell strainer (Pluristrainer). Following centrifugation of the cells (300×g at room temperature) they were washed once in PBS and then digested with Accutase (STEMCELL Technologies) for 20-30 min at 37°C to obtain single cell suspension. After centrifugation, the cell pellet was lysed with ammonium chloride solution (310 mM NH4Cl, 23.8 mM NaHCO3 and 0.2 mM EDTA) for 3 min followed by adding 2.5× volume of PBS + 2% fetal bovine serum (FBS) and centrifuged at 300×g for 5 min (at room temperature) to remove red blood cells. Epithelial cells collected were washed twice in Hank's Balanced Salt Solution (HBSS) + 2% FBS with centrifugation at (200×g at 4°C), then resuspended in HBSS and passed through Flowmi cell strainers (40 µm, Bel-Art) to prepare single cells. 3000 cells were used for scRNA-seq using the 10x Genomics Chromium system.
Libraries generated from single cells according to the manufacturer's protocol for 10X Genomics Chromium Single Cell 3' Reagent Kits v2 (for AXH005 and AXH007) or 10X Genomics Chromium Single Cell 3' Reagent Kits v3 (for AXH019 and AXH020)

value: human efferent duct tissue

tag: Sex

value: male

tag: disease state

value: normal


title: human caput tissue, scRNAseq

description: 10x Genomics

source_name: human caput tissue

value: human caput tissue


title: Day 7 + Diff. medium rep1

description:
d7.+.diff_rep1
31_3931Nantes_s16_CD14-J7plus_A_RNASeq_hs_i2

source_name: Day 7 + Diff. medium_PBMC

value: healthy donor

value: PBMC

value: Day 7 + Diff. medium


title: Tag8F5_Tag01


title: Day 3 - Diff. Medium rep3

description:
d3.-.diff_rep3
27_3931Nantes_s10_CD14-J3_C_RNASeq_hs_i23

source_name: Day 3 - Diff. Medium_PBMC

value: CD14+ pre-monocytes

value: Day 3 - Diff. Medium


title: MS13 CSF

city: Chapel Hill

first: John

last: Wrobel

state: NC

address: 120 Mason Farm Rd

department: Department of Biochemistry and Biophysics

institute: University of North Carolina

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the 10x Genomics Cell Ranger software v5.0.0 analysis pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CSF

extract_protocol:
CSF and blood samples from two RRMS patients were sorted for IL-11R+ cells following RBC lysis for blood samples. In order to decrease batch-to-batch variations, all samples from each experiment were submitted for scRNAseq on the same day.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3' Reagent kit v3 as per manufacturer’s instructions. Library quality control was assessed using Agilent TapeStation for sizing (bp) and KAPA qPCR for concentration. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on the Illumina NovaSeq6000 sequencer in a paired-end, single indexing run.  Sequencing depth targeted 20000 mean reads per cell.

value: CSF

value: IL-11R+ FACS sorted CSF cells

value: RRMS


title: MS12 CSF

description: 10x Genomics


title: MS13 PBMC

description: 10x Genomics

source_name: blood

value: blood

value: IL-11R+ FACS sorted PBMC cells


title: Tag8F4_Tag01

value: CD11b+ cells


title: MS12 PBMC

description: 10x Genomics


title: Tag8F3_Tag01


title: Day 3 - Diff. Medium rep2

description:
d3.-.diff_rep2
26_3931Nantes_s10_CD14-J3_B_RNASeq_hs_i22


title: MS38 IL11 stim

description: 10x Genomics

extract_protocol:
Blood samples from three recently diagnosed untreated RRMS patients were lysed with RBC lysis buffer (eBioscience) following manufacturer’s instructions. Cells stained for IL-11R and sorted using FACS Aria fusion were stimulated with 100 ng/ml rh IL-11 (R&D Systems) for 1 hour or kept unstimulated. In order to decrease batch-to-batch variations, all samples from each experiment were submitted for scRNAseq on the same day.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3' Reagent kit v3 as per manufacturer’s instructions. Library quality control was assessed using Agilent TapeStation for sizing (bp) and KAPA qPCR for concentration. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on the Illumina NovaSeq6000 sequencer in a paired-end, single indexing run.  Sequencing depth targeted 20000 mean reads per cell.

value: IL11 stim


title: MS39 unstim

description: 10x Genomics

value: unstim


title: MS39 IL11 stim

description: 10x Genomics


title: Day 3 - Diff. Medium rep1

description:
d3.-.diff_rep1
25_3931Nantes_s10_CD14-J3_A_RNASeq_hs_i21


title: MS38 unstim

description: 10x Genomics


title: Tag8F11_Tag01


title: MS37 IL11 stim

description: 10x Genomics


title: Day 10 + diuron rep3

description:
d10.Diuron_rep3
12_4126Nantes_CD14-J10-Diuron-3_RNASeq_mm_i12

source_name: Day 10 + diuron_PBMC

value: Day 10 + diuron


title: MS37 unstim

description: 10x Genomics


title: Tag8F1_Tag01


title: Tag8E9_Tag01


title: Day 10 + diuron rep2

description:
d10.Diuron_rep2
11_4126Nantes_CD14-J10-Diuron-2_RNASeq_mm_i11


title: Late Recurrence, Patient 13, Pre-Chemo

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

data_processing:
Base calling was conducted using NovaSeq Control Software, converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software
Sequence reads were trimmed for adaptor sequences using Skewer v.0.2.2
Trimmed sequence reads were mapped to Ensembl GRCh37 and quantified using Kallisto v.0.44
Ensembl gene IDs were converted to HGNC symbols in R using biomaRt v.2.52.0
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include raw count values for each sample
Supplementary files format and content: tab-delimited text files include log2(TPM) values for each sample
Supplementary files format and content: tab-delimited text files indicating each patient's recurrence class and time of sequencing information for each sample

source_name: Ovary

extract_protocol:
The Chemagic360 system (Perkin Elmer) was used to extract total nucleic acid from the tumor samples with TURBO Dnase (Invitrogen) treatment to obtain pure RNA
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KAPA Biosystem, Wilmington, MA) for Illumina following manufacturer's protocols.

value: Ovary

value: Carboplatin + Taxol (6 cycles)

tag: time

value: Pre-Chemo

tag: patient id

tag: recurrence

value: Late

value: HGSOC


title: Late Recurrence, Patient 13, Post-Chemo

value: Post-Chemo


title: Early Recurrence, Patient 11, Post-Chemo

value: Early


title: Day 10 + diuron rep1

description:
d10.Diuron_rep1
10_4126Nantes_CD14-J10-Diuron-1_RNASeq_mm_i10

value: healthy donor

value: PBMC

value: CD14+ pre-monocytes


title: Early Recurrence, Patient 11, Pre-Chemo


title: Early Recurrence, Patient 10, Post-Chemo


title: Late Recurrence, Patient 12, Post-Chemo


title: Day 10+ DMSO rep2

description:
d10.DMSO_rep2
08_4126Nantes_CD14-J10-DMSO-2_RNASeq_mm_i8

source_name: Day 10+ DMSO_PBMC

value: Day 10+ DMSO


title: Early Recurrence, Patient 10, Pre-Chemo


title: Tag8E7_Tag01


title: Late Recurrence, Patient 12, Pre-Chemo


title: Tag8E6_Tag01


title: Day 10+ DMSO rep3

description:
d10.DMSO_rep3
09_4126Nantes_CD14-J10-DMSO-3_RNASeq_mm_i9


title: Tag8E8_Tag01


title: Late Recurrence, Patient 11, Post-Chemo


title: Day 10+ DMSO rep1

description:
d10.DMSO_rep1
07_4126Nantes_CD14-J10-DMSO-1_RNASeq_mm_i7


title: Late Recurrence, Patient 11, Pre-Chemo


title: Day 3 + diuron rep3

description:
d3.Diuron_rep3
06_4126Nantes_CD14-J3-Diuron-3_RNASeq_mm_i6

source_name: Day 3 + diuron_PBMC

value: Day 3 + diuron


title: Tag8E4_Tag01


title: Late Recurrence, Patient 10, Post-Chemo


title: Late Recurrence, Patient 10, Pre-Chemo


title: Day 3 + diuron rep1

description:
d3.Diuron_rep1
04_4126Nantes_CD14-J3-Diuron-1_RNASeq_mm_i4


title: Tag8E3_Tag01


title: Day 3 + diuron rep2

description:
d3.Diuron_rep2
05_4126Nantes_CD14-J3-Diuron-2_RNASeq_mm_i5


title: Late Recurrence, Patient 9, Pre-Chemo


title: Day 3 + DMSO rep3

description:
d3.DMSO_rep3
03_4126Nantes_CD14-J3-DMSO-3_RNASeq_mm_i3

source_name: Day 3 + DMSO_PBMC

value: Day 3 + DMSO


title: Late Recurrence, Patient 8, Pre-Chemo


title: Tag8E11_Tag01

value: CD11b+ cells


title: Tag8E5_Tag01


title: Early Recurrence, Patient 9, Post-Chemo


title: Early Recurrence, Patient 9, Pre-Chemo


title: Early Recurrence, Patient 8, Post-Chemo


title: Early Recurrence, Patient 8, Pre-Chemo


title: Day 3 + DMSO rep2

description:
d3.DMSO_rep2
02_4126Nantes_CD14-J3-DMSO-2_RNASeq_mm_i2


title: Early Recurrence, Patient 7, Post-Chemo


title: Tag8E1_Tag01


title: Early Recurrence, Patient 6, Post-Chemo


title: Early Recurrence, Patient 7, Pre-Chemo


title: Tag8D9_Tag01


title: Day 3 + DMSO rep1

description:
d3.DMSO_rep1
01_4126Nantes_CD14-J3-DMSO-1_RNASeq_mm_i1


title: Tag8E2_Tag01


title: Late Recurrence, Patient 8, Post-Chemo


title: Late Recurrence, Patient 9, Post-Chemo


title: lncMGC_KO, TGF-ß, rep3 [RNA-seq]

city: Duarte

first: Zhuo

last: Chen

address: 1500 E. Durate Rd.

institute: City of Hope

data_processing:
Raw sequences were aligned to the mouse reference genome mm10 using TopHat v2.1.17with default parameters
Gene-level expression levels of all the mouse RefSeq genes  were counted using htseq-count8 v 0.11.2 with settings -s reverse (strand-specific) and -a 10 (filtrating poor alignment reads)
Assembly: mm10
Supplementary files format and content: tab-delimated file for each sample contains read count for each RefSeq gene.

source_name: kidney mesangial cells

growth_protocol: Roswell Park Memorial Institute medium 1640 medium supplemented with 10% fetal bovine serum at 37C 5%CO2.

extract_protocol:
Qiagen's RNA extraction kit.
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol

treatment_protocol: 10 ng/ml  TGF-β (R&D Systems) for 24 hours

value: kidney mesangial cells

value: lncMGC knockout

value: TGF-ß

value: 24 hours


title: Early Recurrence, Patient 6, Pre-Chemo

value: Ovary

value: Carboplatin + Taxol (6 cycles)


title: Early Recurrence, Patient 5, Post-Chemo


title: Tag8D8_Tag01


title: lncMGC_KO, TGF-ß, rep2 [RNA-seq]


title: Early Recurrence, Patient 5, Pre-Chemo

value: Pre-Chemo


title: Tag8D6_Tag01


title: lncMGC_KO, TGF-ß, rep1 [RNA-seq]


title: Tag8D5_Tag01


title: Late Recurrence, Patient 6, Post-Chemo

value: Late

value: HGSOC


title: lncMGC_KO, SD, rep3 [RNA-seq]

value: SD


title: Late Recurrence, Patient 7, Pre-Chemo


title: Late Recurrence, Patient 7, Post-Chemo

value: Post-Chemo


title: Tag8D4_Tag01


title: Late Recurrence, Patient 5, Post-Chemo


title: Late Recurrence, Patient 6, Pre-Chemo


title: Late Recurrence, Patient 5, Pre-Chemo


title: lncMGC_KO, SD, rep2 [RNA-seq]


title: Tag8D3_Tag01


title: M_HJZ_XDL_3

city: Nanjing

first: Jun

last: Kang

address: Xiaoling Wei Street

country: China

institute: Nanjing Agricultural Unversity

data_processing:
For data analysis, all related information was transformed into raw data after online sequencing, removing the low quality, linker contamination and reads with unknown base N content to obtain clean reads. Clean reads were mapped to the V. vinifera reference genome (ftp://ftp.ensemblgenomes.org/pub/release-23/plants/gtf/vitis_vinifera/) by using HISAT2 (Gong et al. 2022)
The mapped fragments for each gene were counted by featureCounts and transcripts per million (TPM) were calculated. Genes with averaged TPM (replicates = 3) were considered expressed.
Supplementary files format and content: Tab-delimited text file including TPM values for each sample

organism: Vitis vinifera

source_name: M-HJZ

extract_protocol:
Total RNA was extracted separately with the Trizol   (Invitrogen) method following the steps as described   in instructions. Te genomic DNA was digested using   DNase (TAKARA, Dalian, China).
MRNA libraries were constructed for each sample and sequenced using the Illumina HiSeq-2000 platform.

value: fruit

tag: developmental stage

value: maturity

tag: ecological zone

value: HJZ


title: Early Recurrence, Patient 4, Post-Chemo

value: Early


title: Genomic DNA from whole blood sample [SUAZ_052_meth_v1]

source_name: PESA study participant SUAZ_052_meth_v1

tag: gender

value: Male

value: Intermediate


title: lncMGC_KO, SD, rep1 [RNA-seq]

value: kidney mesangial cells


title: Tag8D2_Tag01

value: CD11b+ cells

tag: age


title: Early Recurrence, Patient 4, Pre-Chemo


title: WT, TGF-ß, rep3 [RNA-seq]

value: WT

value: TGF-ß


title: Late Recurrence, Patient 4, Pre-Chemo

value: Ovary


title: WT, TGF-ß, rep2 [RNA-seq]

value: 24 hours


title: Tag8D1_Tag01


title: Early Recurrence, Patient 3, Post-Chemo

value: Carboplatin + Taxol (6 cycles)


title: Late Recurrence, Patient 3, Pre-Chemo

value: Pre-Chemo

value: Late


title: WT, TGF-ß, rep1 [RNA-seq]


title: Late Recurrence, Patient 3, Post-Chemo

value: HGSOC


title: Early Recurrence, Patient 3, Pre-Chemo


title: Late Recurrence, Patient 2, Post-Chemo

value: Post-Chemo


title: WT, SD, rep3 [RNA-seq]

value: SD


title: Late Recurrence, Patient 2, Pre-Chemo


title: Early Recurrence, Patient 2, Post-Chemo


title: Early Recurrence, Patient 1, Post-Chemo


title: Early Recurrence, Patient 2, Pre-Chemo


title: WT, SD, rep2 [RNA-seq]


title: Tag8C4_Tag01


title: WT, SD, rep1 [RNA-seq]


title: Tag8C2_Tag01


title: Early Recurrence, Patient 1, Pre-Chemo


title: Late Recurrence, Patient 1, Post-Chemo


title: Control HEK293, no ligand addition rep1

city: Bethesda

first: Kiersten

middle: Sierra

last: Campbell

state: MD

address: 9000 Rockville Pike

institute: NICHD

data_processing:
Raw sequence reads were processed using lcdb-wf (lcdb.github.io/lcdb-wf/) according to the following steps. Raw sequence reads were trimmed with cutadapt v3.4  to remove any adapters while performing light quality trimming with parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 –minimum-length = 25.’
Sequencing library quality was assessed with fastqc v0.11.9 with default parameters. The presence of common sequencing contaminants was evaluated with fastq_screen v0.14.0 with parameters ‘–subset 100000 –aligner bowtie2.’ Trimmed reads were mapped to the Homo sapiens reference genome (Gencode release 28) using STAR v2.7.8a.
Multimapping reads were filtered using samtools v1.12 .
Uniquely aligned reads were then counted in genes with the featureCounts program of the subread package v2.0.1 using Homo sapiens reference (Gencode release 28) annotations .
Assembly: hg38
Supplementary files format and content: tab-delimited text file including featurecounts raw counts

extract_protocol:
RNA extracted according to the Qiagen RNAeasy mini kit
PolyA libraries prepared according to Illumina TruSeq stranded mRNA protocol

treatment_protocol: Cells were serum-starved for 3h, then treated with 1µM 5-HT for 1h

value: Control


title: lncMGC_KO, TGF-ß, rep1 [ATAC-seq]

library_source: genomic

data_processing:
Basecalls were performed using real-time analysis (RTA) 2.2.38 .
The adaptors of ATAC-seq reads were trimmed using cutadapt v.1.9.1
ATAC-seq reads were aligned to the UCSC mm10 genome using BWA version 0.7.5a-r405.
Reads are filtered out if located on mitochondrial, not properly paired, of pair-end length > 2kb, mapping quality < 20 or duplicated reads using samtools
Bedgraph file for each sample were generated on the aligned paired reads and scaled to 50 million total reads.
Assembly: mm10
Supplementary files format and content: Compressed Bedgraph file of scaled coverage for each sample

extract_protocol:
Qiagen's RNA extraction kit.
Omni-ATAC protocol was used as described (M Ryan Corces, Nature method 2017) for cell lysis, tagmentation, and DNA purification. The Tn5 treated DNA was amplified with 10 cycles of PCR in 50μl reaction volumes.

value: lncMGC knockout

tag: molecule subtype

value: Genomic DNA treated Tn5 transposase


title: lncMGC_KO, TGF-ß, rep2 [ATAC-seq]


title: Control HEK293, serotonin treated rep2

value: Serotonin


title: lncMGC_KO, TGF-ß, rep3 [ATAC-seq]


title: Tag8C5_Tag01


title: Tag8C11_Tag01


title: Tag8C1_Tag01


title: lncMGC_KO, SD, rep3 [ATAC-seq]


title: Control HEK293, serotonin treated rep1


title: Late Recurrence, Patient 1, Pre-Chemo


title: Late Recurrence, Patient 4, Post-Chemo


title: HTR1E overexpressing HEK293, serotonin treated rep2


title: Tag8C8_Tag01


title: HTR1E overexpressing HEK293, no ligand addition rep2


title: HTR1E overexpressing HEK293, serotonin treated rep1


title: lncMGC_KO, SD, rep2 [ATAC-seq]


title: HTR1E overexpressing HEK293, no ligand addition rep1


title: Tag8B6_Tag01


title: Tag8B3_Tag01


title: Control HEK293, no ligand addition rep2


title: PBMC sample gd TCR

city: Beijing

first: Ruoyu

last: Zhang

address: Life Science Park building 1 B220

institute: Innovec Biotherapeutics

data_processing:
Raw sequencing data were processed by Cell Ranger version 7.0.1 (10X Genomics) to generate gene expression matrix and assemble TCR sequences with human GRCh38 reference genome. scRNA-seq data analysis were performed with Scanpy. In quality control step, cells were filtered by the following criteria: 1) mitochondrial abundance < 15%, 2) minimum gene detected > 500, 3) Maximum UMI < 40000. Potential doublets were detected and removed by Scrublet4. Principal component analysis (PCA) was applied on the highly variable genes. Batch effects were corrected using Harmony
Assembly: human GRCh38
Supplementary files format and content: 10X matrix
Library strategy: scTCR-seq

source_name: PBMC

extract_protocol: On the date of experiment, the cells were thawed using a water bath at 37°C and loaded into Chromium microfluidic chips and barcoded within a 10X Chromium Controller (10X Genomics, US). For transcriptome, procedures were performed with reagents: Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (10X Genomics, PN-1000263). TCR enrichment was carried out using the Chromium Single Cell Human TCR Amplification Kit (10X Genomics, PN-1000252) for αβ transcripts, or customer primers for γδ TCR transcripts2. All the libraries were sequenced on the NovaSeq 6000 platform (Illumina, US)

value: post-treatment

value: PBMC

tag: sequencing

value: TCR-seq gd TCR

tag: tcr enrichment

value: γδ transcripts


title: lncMGC_KO, SD, rep1 [ATAC-seq]

tag: cell type

value: kidney mesangial cells


title: bone marrow sample gd TCR

source_name: BM

tag: treatment

tag: tissue

value: bone marrow


title: Tag8B2_Tag01

value: CD11b+ cells

tag: strain


title: WT, TGF-ß, rep3 [ATAC-seq]

tag: genotype

value: WT


title: Tag8B1_Tag01


title: bone marrow sample RNA-seq

data_processing:
Raw sequencing data were processed by Cell Ranger version 7.0.1 (10X Genomics) to generate gene expression matrix and assemble TCR sequences with human GRCh38 reference genome. scRNA-seq data analysis were performed with Scanpy. In quality control step, cells were filtered by the following criteria: 1) mitochondrial abundance < 15%, 2) minimum gene detected > 500, 3) Maximum UMI < 40000. Potential doublets were detected and removed by Scrublet4. Principal component analysis (PCA) was applied on the highly variable genes. Batch effects were corrected using Harmony
Assembly: human GRCh38
Supplementary files format and content: 10X matrix

value: RNA-seq


title: 8-TI2-A030

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

data_processing:
Reads were quantified by kallisto version 42.5, using Gencode v24 as the reference genome
Data was filtered to includ mRNAs  with TPM above 1 in 20% of the samples.
Assembly: Gencode v24
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Terminal ileum

extract_protocol:
RNA was isolated from biopsies using the Qiagen AllPrep RNA/DNA Mini Kit.
PolyA-RNA selection, fragmentation, cDNA synthesis, adaptor ligation, TruSeq RNA sample library preparation (Illumina, San Diego, CA), and paired-end sequencing was performed.

value: Terminal ileum

tag: diagnosis

value: Female


title: PBMC sample RNA-seq


title: bone marrow sample ab TCR

value: TCR-seq ab TCR

value: αβ transcripts


title: WT, TGF-ß, rep2 [ATAC-seq]


title: PBMC sample ab TCR


title: 71-A061-TI1

value: Control


title: WT, SD, rep3 [ATAC-seq]


title: 75-A063-TI2

value: CD


title: WT, TGF-ß, rep1 [ATAC-seq]

value: Genomic DNA treated Tn5 transposase


title: 62-A058-TI2


title: Tag8A2_Tag01


title: WT, SD, rep2 [ATAC-seq]


title: 6-TI2-A028


title: 60-A057-TI2

value: Male


title: Tag8A3_Tag01


title: 56-A056-TI1


title: Tag8A4_Tag01


title: WT, SD, rep1 [ATAC-seq]


title: 50-A052-TI1


title: Tag8A12_Tag01


title: 47-A051-TI2


title: NDRG1-EGFP LMNA KO rep3-2

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Initial quality analyses were performed on FastQ files before trimming using FASTQC (Andrews, 2010). To trim and filter low quality reads, fastp (Chen et al., 2018) processor was used. High-quality reads were aligned to the mouse reference genome (mm10) by splice-aware aligner HISAT2 (Kim et al., 2015). Obtained BAM files of mapped single-end reads sorted by genomic coordinates using samtools (v1.4.1) (Li et al., 2009). Raw counts were generated with the NCBI mouse RefSeq annotation (build 38), using uniquely aligned reads to exons by the featureCounts tool (Rsubread v2.12.0) (Liao et al., 2014). The raw read counts were input into DESeq2 (v1.38.1) (Anders and Huber, 2010), for normalizing the signal for each transcript and to ascertain differential gene expression with associated p-values. We used a cut-off of p-value < 0.05 to identify differentially expressed genes. Gene ontology analysis and Gene Set Enrichment Analysis were performed using clusterProfiler (Yu et al., 2012) and GSEA (Subramanian et al., 2005), respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each technical replicate

source_name: sorted  myelinating oligodendrocytes

growth_protocol:
Mouse breeding scheme to obtain desired populations of sorted cells: The myelinating oligodendrocyte reporter line Ndrg1-EGFP mice (Marechal et al., 2021) were bred with  Cnp+/+;Lmnafl/fl  mice to obtain NDRG1-EGFP LMNA WT)  or with CnpCre/+;Lmnafl/fl mice  to obtain NDRG1-EGFP LMNA KO.
Oligodendrocytes were sorted from 8weeks NDRG1_EGFP-LMNA WT and KO brains, using fluorescence-activated cell sorting as described (Moyon et al., 2021). Tissue was dissected in HBSS 1X (HBSS 10X (Invitrogen), 0.01 M HEPES buffer, 0.75% sodium bicarbonate (Invitrogen), and 1% penicillin/streptomycin) and mechanically dissociated. After an enzymatic dissociation step using papain (30 μg/ml in DMEM-Glutamax, with 0.24 μg/ml L-cysteine and 40 μg/ml DNase I), samples were layered over a pre-formed Percoll density gradient and then centrifuged for 15 min. Cells were then collected and stained with propidium iodide (PI) for 2 min at room temperature (RT) to exclude dead cells. In a second step, GFP-positive and PI-negative cells were sorted by fluorescence-activated cell sorting (FACS; Aria, Becton Dickinson) and collected in pure fetal bovine serum.

extract_protocol:
RNA from cells were extracted from three biological replicates for each condition using TRIzol (Invitrogen) extraction and isopropanol precipitation. RNA samples were resuspended in nuclease-free H2O and further purified with RNeasy Mini Kit (Qiagen,  74106) with on-column DNase treatment. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop.
For RNA-sequencing, approximately 5.2 ng of total RNA per sample was used for library construction with the Ultra-Low-RNA-seq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument according to the manufacturer’s instructions for 50 bp single-end read runs.

value: myelinating oligodendrocytes

value: postnatal day 60

value: CnpCre/+;Lmnafl/fl


title: Tag8C3_Tag01


title: Tag8A6_Tag01


title: 72-A062-TI2


title: Tag7H9_Tag01


title: 39-A047-TI2


title: 35-TI1-A045


title: 45-A050-TI2


title: 29-TI1-A042


title: Tag7H7_Tag01


title: replicate 3, MERFISH

type: RNA

description: panel of 287 genes was measured by MERFISH

data_processing:
Encoded MERFISH images were processed according to manufacturer's pipeline (https://vizgen.com/technology/#merfish). The output of this pipeline are spatial positions of individual transcripts and segmented single cells based on DAPI and poly-A stainings. Single cell expression tables are produced by counting individual transcripts within segmented cell boundaries.
Tab-separated single cell expression matrix and cell metadata

source_name: MERFISH

extract_protocol:
18 days after LPC injection, mice were anaesthetized with an i.p. injection of MMF (fentanyl (0.05 mg/kg)–midazolam (5 mg/kg)–medetomidine (1 mg/kg)) and transcardially perfused with 2 UI/mL Heparin (Heparin-Natrium-25000-ratiopharm®, PZN: 03029843) in HBSS (no calcium, no magnesium, Gibco™, 14175129) for 3 min and 4 % paraformaldehyde (PFA, EM Grade, Electron Microscopy Sciences, Cat. No. 15710, diluted in 10X PBS, Invitrogen™, AM9624 and UltraPure™ Distilled Water, Invitrogen™, 10977-035) for 5 min, before carefully removing the brain from the skull. Afterwards, the brains were fixed by submergingin 4% PFA for 6 hours, followed by 14 hours in 15% sucrose (Sigma-Aldrich, S0389 in UltraPure™ Distilled Water, Invitrogen™, 10977-035) and 5 hours in 30% sucrose. Next, the PFA-fixed brains were simultaneously embedded in Tissue-Tek® O.C.T.™ Compound (Sakura, 4583) and frozen in a plastic mold on dry ice. For the fresh frozen brain samples, the mouse was only perfused with Heparin in HBSS and directly embedded and frozen in Tissue-Tek® O.C.T.™ Compound on dry ice. Brains were stored at -80°C until further processing. Coronal, 10 µm thick brain sections were prepared and collected at a cryotome (CryoStar NX70, Thermo Scientific). Sections determined for MERFISH analysis were placed on round glass slides provided by Vizgen Corp. (Cambridge, MA 02138) and functionalized in-house by coating one side with a 0.1 mg/mL poly-L-ornithine solution (Sigma-Aldrich, P4957 in PBS) for 1 hour, before drying them. Brain sections for MERFISH were subsequently washed two times with PBS and one time with 70 % ethanol (VWR Chemicals, 20.821.310, diluted in UltraPure™ Distilled Water, Invitrogen™) for 5 minutes each. Then samples were individually sealed in bags filled with 70 % ethanol and shipped to Vizgen Corp. (Cambridge, MA 02138) for MERFISH analysis.
MERFISH
Brain sections were measured by MERFISH according to manufacturer's protocol (https://vizgen.com/technology/#merfish)

value: brain cells

value: Brain

value: 18 weeks

tag: molecule

value: other

tag: instrument model

value: Vizgen


title: Tag8A1_Tag01

value: CD11b+ cells


title: NDRG1-EGFP LMNA KO rep1-2


title: NDRG1-EGFP LMNA KO rep3-1


title: NDRG1-EGFP LMNA KO rep2-1


title: NDRG1-EGFP LMNA KO rep2-2


title: NDRG1-EGFP LMNA KO rep1-1


title: NDRG1-EGFP LMNA WT rep3-2

value: Cnp+/+;Lmnafl/fl


title: replicate 1, MERFISH


title: 18-TI1-A035

value: Terminal ileum


title: NDRG1-EGFP LMNA WT rep3-1


title: Tag7H6_Tag01


title: 33-TI2-A044


title: Tag7H8_Tag01


title: 28-TI2-A041


title: Tag7H5_Tag01


title: 14-TI1-A033


title: Tag7H3_Tag01


title: Tag7H4_Tag01


title: NDRG1-EGFP LMNA WT rep2-2


title: 25-TI1-A040


title: Tag7H2_Tag01


title: 12-TI2-A032

value: Female


title: 21-TI1-A036


title: 1-TI2-A017


title: NDRG1-EGFP LMNA WT rep2-1


title: 36hpi, ptetEUo, rep1

city: Irvine

first: Syed

middle: Meraj Azhar

last: Rizvi

address: University of California Irvine

department: Microbiology and Molecular Genetics

country: India

institute: University of California Irvine

description: test strain

data_processing:
The intensities of the spots on the images and the base calls are computed directly during the run using Illumina’s Real Time Analysis (RTA) software installed on a computer located in the UCI-GHTF.
Reads were mapped to C. trachomatis L2 434/Bu genome and reads were counted for annotated genes on Qiagen CLC Genomics Workbench (version 21.0.5) software with high stringency settings (mismatch cost 2, and insertion and deletion cost 3, length and similarity fraction 0.8 each, maximum number of hits for a read to 10, and minimum read count fusion table to 5).
Assembly: GCA_000068585.1
Supplementary files format and content: Each processed data file corresponding to the libraries is an Excel (.xlsx) file containing name of C. trachomatis genes, chromosome, region, expression value, TPM value, RPKM value, gene length, unique gene reads, and total gene reads
Supplementary files format and content: Processed data file (Total counts_pBOMBVsEuo.xlsx) is an Excel (.xlsx) file containing the name of C. trachomatis genes, total mapped read counts, and average read counts for each sample

organism: Chlamydia trachomatis

source_name: HeLa

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

extract_protocol:
C. trachomatis infected HeLa were disolved in TRIzol (300 ul/ well in 24 well plate). After centrifugation, the aqueous layer containing the total RNA was loaded on the Qiagen column and supplier instructions were followed hereafter. RNA was DNase treated on the column and eluted in MQ water. After RNA extraction, the samples were analyzed by Qubit to check for any degradation of the RNA. The yield of the RNA samples was measured on a Qubit.
RNASeq library prepared using Zymo-seq RiboFree Total RNA Library Kit by Zymo Research, with 10ng of total RNA

tag: cell line

value: HeLa

value: Epithelial cell

value: 15nM anhydrotetcycline


title: 36hpi, ptetEuo, rep2

description: test strain


title: Tag7H12_Tag01


title: replicate 2, MERFISH


title: 36hpi, pBOMB, rep2

description: control strain


title: 36hpi, pBOMB, rep1

description: control strain


title: Tag7H11_Tag01


title: NDRG1-EGFP LMNA WT rep1-2


title: NDRG1-EGFP LMNA WT rep1-1


title: Tag8C6_Tag01


title: 32hpi, ptetEuo, rep2

description: test strain


title: FoB_BR4

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
Reads were trimmed using Trim Galore and mapped to mouse genome GRCm38 using HiSat2 (2.1.0), including known splice sites from the Ensembl annotation release 90
The normalised counts in transcripts per kilobase million (TPM), which corrects for transcript length and library size, were calculated using StringTie (2.1.1), using the Ensembl GRCm38 annotation release 90
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files showing names, IDs and coordinates of genes together with their coverage, FPKM and TPM calculated using StringTie

source_name: follicular B cells

growth_protocol: Single cell suspensions were prepared from spleen by passing the organ through a 70mm cell strainer. B cells were pre-enriched through negative selection (Miltenyi B cell isolation kit, cat # 130-090-862) and T1, T2, MZ and FoB cell subsets FACS-sorted using anti-CD19 (6D5), anti-CD93 (AA4.1), anti-CD23 (B3B4), anti-CD21 (7G6) and anti-IgM (II/41) antibodies.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
cDNA was generated from polyadenylated transcripts using SMART-Seq® v4 Ultra® Low Input RNA Kit (cat # 634891, Takara Bio). mRNAseq libraries were prepared with Nextera XT DNA Library Preparation Kit (cat# FC-131–1096, Illumina) and quantified using KAPA library quantification kit (Roche). mRNA-seq libraries were run on a HiSeq 2500 RapidRun generating 50bp single-end reads.

treatment_protocol: B cell subsets were purified from 12-week old untreated mice

tag: Sex

value: male

value: spleen

tag: flow cytometry markers

value: follicular B cells


title: Tag7H1_Tag01


title: 32hpi, ptetEUo, rep1

description: test strain


title: FoB_BR3

value: female


title: 32hpi, pBOMB, rep2

description: control strain


title: FoB_BR2


title: Tag7G9_Tag01


title: 32hpi, pBOMB, rep1

description: control strain


title: FoB_BR1


title: 28hpi, ptetEuo, rep2

description: test strain


title: Tag7G7_Tag01


title: HRMEC_siLGALS1_1

city: Wuhan

first: Ning

last: Yang

address: 238# Jiefang Road

institute: Renmin Hospital of Wuhan University

data_processing:
Illumina bcl2fastq software used for basecalling. 3' adapter and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
The dataset containing the clean reads was aligned to the GRch38 genome by tophat2 allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
DESeq2 was used to analyze the differential expression between two or more samples, and the analysis results can be used to determine whether a gene is differentially expressed by fold change(FC) and false discovery rate(FDR).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

source_name: LGALS knockdown in HRMEC

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: HRMEC

value: human retinal microvascular endothelial cells

value: LGALS knockdown


title: 10-TI2-A031

value: Control

value: Male


title: HRMEC_siLGALS1_3


title: HRMEC_NC_3

source_name: HRMEC (control plasmid)

value: WT


title: HRMEC_siLGALS1_2


title: HRMEC_NC_1


title: 28hpi, ptetEUo, rep1

description: test strain


title: MZ_BR4

source_name: marginal zone B cells

value: marginal zone B cells


title: Tag7G6_Tag01

data_processing:
Fastq files were quality-controlled with FastQC and reads were then aligned using rnaSTAR to the GRCm38 (mm10) genome with addition of ERCC spike-in sequences. To obtain single cell gene expression matrices reads were counted with rnaSTAR using parameter “quantMode GeneCounts” and unstranded argument.
Assembly: mm10
Supplementary files format and content: Tab-separated counts per cell and cell metadata

extract_protocol:
18 days after LPC injection, mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; gray matter was isolated from the frontal cortex and white matter was isolated form optic tract, medial lemniscus and corpus callosum (attached gray matter and choroid plexus were carefully removed). Single cells were isolated using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D to a final concentration of 45 mM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. The dissociated cell suspension was passed through a 70 mm cell strainer before labeling. Subsequently, cells were blocked with mouse FcR-blocking reagent (CD16/CD32 Monoclonal Antibody) and then stained for with the antibodiy against CD11b (PE/Cy7,M1/70, eBioscience, Cat:48-0451-82,1:200) and afterwards washed with PBS (Sigma, D8537). Cells were then stained with DAPI (4’,6-diamidino-2-phenylindole, 1:10000 dilution; Sigma)  and viable (DAPI-negative) single CD11b-positive cells were sorted by flow cytometry (SH800; Sony) into 96 well plates filled with 4 mL lysis buffer containing 0.05% Triton X-100 (Sigma) and, ERCC spike-in Mix (1:24000000 dilution), 2.5 mM oligo-dT, 2.5 mM dNTP and 2 U/mL of recombinant RNase inhibitor (Clontech).
The 96-well plates containing the sorted single cells were thawed and incubated for 3 min at 72°C and thereafter immediately placed on ice. To perform reverse transcription (RT) we added into each well a master mix of 0.59 μL H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μL Recombinant RNase Inhibitor (Clontech), 2 μL Betaine (5 M Sigma), 0.5 μL DTT (100 mM) 0.06 μL MgCl2 (1 M Sigma), 0.1 μL Templateswitching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next RT reactions were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; ending with 70°C for 5 min for enzyme inactivation. Preamplification of cDNA was performed by adding 12.5 μL KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μL H2O, 0.25 μL ISPCR primers (10 μM, 5’ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μL Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 23 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure beads (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Libraries were assessed by Bio-analyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and quantified using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies). Further selection of samples was performed via qPCR assay against ubiquitin transcripts Ubb77 (primer 1 5’-GGAGAGTCCATCGTGGTTATTT-3’ primer 2 5’-ACCTCTAGGGTGATGGTCTT-3’, probe 5’-/5Cy5/TGCAGATCTTCGTGAAGACCTGAC/3IAbRQSp/-3’) measured on a LightCycler 480 Instrument II (Roche). Samples were normalized to 160 pg/μL. Sequencing libraries were constructed by using in-house produced Tn5 transposase. Libraries were barcoded, pooled and purified in 3 rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library. Libraries were then sequenced with 100 bp paired-end sequencing on DNBSeq platform (BGI group).

value: CD11b+ cells


title: MZ_BR3


title: 28hpi, pBOMB, rep2

description: control strain


title: Tag7G5_Tag01


title: C4

first: enzhi

last: jia

state: Jiangsu Province

address: Guangzhou Road 300

institute: Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University

data_processing:
Transcriptome high throughput sequencing was performed by CloudSeq Biotech (Shanghai, China).
Briefly, total RNA was used for removing the rRNAs with NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).
Library sequencing was performed on an illumina Novaseq 6000 instrument with 150bp paired end reads.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: PBMCs,case,Gensini scores=72

value: WBC

value: peripheral blood mononuclear cells

tag: disease state

value: CAD

tag: gensini scores


title: MZ_BR2


title: 28hpi, pBOMB, rep1

description: control strain

value: HeLa

value: Epithelial cell


title: C5

source_name: PBMCs,case,Gensini scores=168

extract_protocol: RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA)


title: Tag7H10_Tag01

tag: age


title: Tag7G4_Tag01


title: MZ_BR1

value: male


title: HRMEC_NC_2


title: Tag7G8_Tag01


title: Tag7G3_Tag01


title: C3

source_name: PBMCs,case,Gensini scores=100


title: 16hpi, ptetEuo, rep2

description: test strain

value: 15nM anhydrotetcycline


title: C2

source_name: PBMCs,case,Gensini scores=30


title: 16hpi, ptetEUo, rep1

description: test strain


title: T2_BR4

source_name: transitional 2 B cells

value: spleen

value: transitional 2 B cells


title: Tag7G2_Tag01


title: C1

source_name: PBMCs,case,Gensini scores=40


title: T2_BR3

value: female


title: Tag7G12_Tag01


title: T2_BR2


title: 16hpi, pBOMB, rep1

description: control strain


title: N4

source_name: PBMCs,control,Gensini scores=0

value: healthy control


title: 16hpi, pBOMB, rep2

description: control strain


title: Tag7G11_Tag01


title: Tag7G10_Tag01


title: T2_BR1


title: MT, 0.25, SEN CM, 3

city: Dresden

first: Maximina

last: Yun

state: Saxony

address: Fetscherstrasse 105

department: CRTD

institute: TUD

data_processing:
use Galaxy.org
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to the N. viridescens transcriptome using Sailfish
Assembly: N. viridescens transcriptome assembly;  https://sandberglab.se/data/redspottednewt ; 10.1016/j.yexcr.2013.02.013
Supplementary files format and content: csv files include TPM values for each sample

organism: Notophthalmus viridescens

growth_protocol: A1 newt myogenic cells were maintained in 80% MEM supplemented with 10% fetal bovine serum (FBS), insulin, glutamine pen/strep antibiotics in humidified atmosphere with 2% CO2 at 25C before treatment under described experimental conditions.

extract_protocol:
RNeasy micro
RNA was harvested using RNeasy plus kits (Qiagen).
RNA libraries for RNA-seq were prepared using the Illumina DNA Tagmentation kit.

treatment_protocol: Myogenic differentiation and dedifferentiation; 5d 0.25% FCS followed by 3d exposure to 48 hour, filtered senescent cell conditioned media (0.25% FCS). Myotubes purified by size exclusion (aggregates removed using 100 um filter, myotubes collected on 30 um filter).

value: Myogenic limb cells

tag: population

value: A1-derived MT, 0.25, SEN CM

tag: time

value: Day 8


title: N3


title: T1_BR4

source_name: transitional 1 B cells

value: transitional 1 B cells


title: MT, 0.25, SEN CM, 2

value: WT


title: Tag7G1_Tag01

value: CD11b+ cells


title: N2

value: WBC


title: Tag7F9_Tag01


title: MT, 0.25, SEN CM, 1


title: N1

value: peripheral blood mononuclear cells


title: MT, 0.25, PRO CM, 3

treatment_protocol: Myogenic differentiation and dedifferentiation; 5d 0.25% FCS followed by 3d exposure to 48 hour, filtered proliferating cell conditioned media (0.25% FCS). Myotubes purified by size exclusion (aggregates removed using 100 um filter, myotubes collected on 30 um filter).

value: A1-derived MT, 0.25, PRO CM


title: T1_BR2


title: Tag7F8_Tag01


title: T1_BR1


title: N5


title: NKYS WB2

city: Shanghai

first: Jianfeng

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: NKYS

growth_protocol: NKYS cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 100 IU/ml IL-2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: NKYS were treated with DMSO, 50nM WB737 for 24h.

value: NKYS

value: NK/T cell lymphoma


title: Tag7F7_Tag01

first: Peter

address: Feodor-Lynen-Strasse 17

institute: LMU Hospital, Institute for Stroke and Dementia Research


title: NKYS WB1


title: Tag7F5_Tag01


title: NKYS Ctrl2


title: MT, 0.25, PRO CM, 1


title: Tag7F4_Tag01


title: Tag7F3_Tag01


title: NKYS Ctrl1


title: Tag7F12_Tag01


title: 5-TI2-A006

source_name: Terminal ileum

value: Terminal ileum

value: Control

tag: gender

value: Male


title: MT, 10, 2

treatment_protocol: Myogenic differentiation and dedifferentiation; 5d 0.25% FCS followed by 3d 10% FCS. Myotubes purified by size exclusion (aggregates removed using 100 um filter, myotubes collected on 30 um filter).

tag: cell type

value: A1-derived MT, 10


title: 7-TI1-A276-A008

value: CD


title: MT, 10, 1


title: MT, 0.25, 3

treatment_protocol: Myogenic differentiation; 0.25% FCS (5d + 3d). Myotubes purified by size exclusion (aggregates removed using 100 um filter, myotubes collected on 30 um filter).

value: A1-derived MT, 0.25


title: Tag7F11_Tag01


title: MT, 0.25, PRO CM, 2

value: Myogenic limb cells


title: 4-TI2-A004

value: Female


title: Tag7F10_Tag01


title: Naive CD4 T cells from a 22-month-old mouse rep4

city: Paris

first: sebastien

last: jacques

address: 24 rue du faubourg saint jacques

department: Genomic

institute: Institut Cochin

description: Lymph-node cells

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls.  RMA normalization is performed using R with custom CDF EntrezGene version 22 from Brain Array.

label: Biotin

source_name: Cell sorted naive CD4 T cells

label_protocol: After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 pico kit), 700 pg of total RNA is reverse transcribed following the Ovation PicoV2 (TECAN). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Tecan protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen).

value: female


title: MT, 0.25, 2

value: Day 8


title: Naive CD4 T cells from a 22-month-old mouse rep2

description: Lymph-node cells


title: Naive CD4 T cells from a 22-month-old mouse rep3

description: Lymph-node cells


title: Tag7E9_Tag01

city: Munich

last: Androvic


title: 43-TI2-A026


title: SEN, 3

extract_protocol:
RNeasy mini
RNA was harvested using RNeasy plus kits (Qiagen).
RNA libraries for RNA-seq were prepared using the Illumina DNA Tagmentation kit.

treatment_protocol: 24h 20 μM Etoposide + 1 μM nutlin followed by 11 days 1 μM nutlin; 10% FCS.

value: WT

value: A1 cells, SEN

value: Day 12


title: Naive CD4 T cells from a 3-month-old mouse rep1

description: Lymph-node cells


title: MT, 10, 3


title: Naive CD4 T cells from a 3-month-old mouse rep2

description: Lymph-node cells


title: MT, 0.25, 1


title: Tag7E8_Tag01

value: CD11b+ cells


title: Tag7E6_Tag01


title: 48-TI1-A024


title: Tag7E5_Tag01


title: SEN, 2


title: 46-TI2-A027


title: PRO, 3

treatment_protocol: DMSO vehicle only; 10% FCS. Subculture at d6 to avoid confluence.

value: A1 cells, PRO


title: SEN, 1


title: Tag7E4_Tag01


title: Naive CD4 T cells from a 22-month-old mouse rep1

description: Lymph-node cells


title: Naive CD4 T cells from a Foxo1Ctrl (WT) mouse [05_WT-2]

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.

data_processing:
The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls.
RMA normalization is performed using R with custom CDF EntrezGene version 22 from Brain Array.

label_protocol: After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 pico kit), 20 ng of total RNA is reverse transcribed following the Ovation PicoSL V2 (TECAN). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Tecan protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

extract_protocol: RNA was harvested using RNeasy mini plus kit (Qiagen).

value: Foxo1Ctrl (WT)

value: Lymph-nodes

value: Naive CD4 T cells


title: 41-TI2-A022

value: Terminal ileum

value: Control


title: Naive CD4 T cells from a 3-month-old mouse rep3

description: Lymph-node cells


title: Naive CD4 T cells from a Foxo1Ctrl (WT) mouse [04_WT-1]


title: Naive CD4 T cells from a Foxo1Ctrl (WT) mouse [06_WT-3]


title: Naive CD4 T cells from a Foxo1TKO mouse [03_KO-3]


title: PRO, 2


title: Tag7E3_Tag01


title: 32-TI-A020

value: Male


title: 31-TI2-A019


title: Naive CD4 T cells from a Foxo1TKO mouse [02_KO-2]


title: PRO, 1


title: 28-TI2-A018


title: 39-TI1-A025

value: CD


title: 25-TI1-A016


title: Tag7E2_Tag01


title: T1_BR3

value: spleen

value: transitional 1 B cells


title: Tag7E12_Tag01


title: 23-TI2-A015


title: Naive CD4 T cells from a Foxo1TKO mouse [01_KO-1]

value: Female


title: PD3

city: Kansas City

first: Andrew

middle: Joseph

last: Price

state: MO

address: 1000 E. 50th Street

department: Computational Biology

institute: Stowers Institute for Medical Research

description: steady state replicate 3

data_processing:
Illumina bcl2fastq2 v2.18 was used to generate fastq files
Reads were aligned to UCSC genome Nvec200 with STAR aligner (version 2.7.3a), using Ensembl 99 gene models.
TPM and RPKM are calculated using RSEM v1.3.0
Raw Read counts are calculted using STAR (version 2.7.3.a)
Assembly: UCSC genome Nvec200 (https://simrbase.stowers.org/jb_pub/?data=data%2Fstarlet_pub&tracks=NV2g_genes&NV2t_transcripts=&loc=chr15%3A5620252..5627144&highlight)
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

organism: Nematostella vectensis

source_name: physa

extract_protocol:
Total RNA was isolated from all samples using the RNAqueous kit (Ambion) according to the manufacturer’s protocol. Briefly, after  pipetting off and discarding RNAlater from each sample, whole animals were lysed by pipetting in lysis buffer for < 2 min, washed 2–3 times, and eluted on a column. Genomic DNA was removed using DNA-free kit (Invitrogen), and RNA was assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
Sequencing libraries were prepared using TruSeq Stranded mRNA Preparation Kit(Illumina) following the manufacturer’s instructions

value: physa

value: genome Putnam et al. (2007)

tag: state

value: steady state


title: 21-TI2-A014

tag: tissue


title: PD1

description: steady state replicate 1


title: HepG2 cells, RNA_Rep1

city: Huntsville

first: Belle

middle: Aine

last: Moyers

state: AL

address: 601 Genome Way

institute: HudsonAlpha

data_processing:
Association run was mapped to design file using bwa mem version 0.7.17 to identify candidate barcode-element associations.
Barcodes with identical nucleotide strings of length 7 or more were excluded
Barcodes with candidate associations with more than 1 element were discarded.
Barcode-element associations were only kept if at least 2 reads independently supported a given barcode-element association.
Counts were calculated by comparing barcode-element associations in the dictionary with sequence reads. 1 mismatch was allowed, and only unique assignments were considered.
Assembly: hg38
Supplementary files format and content: barcode_element_association_table.txt shows the final supported barcode-element associations after all filtering steps.
Supplementary files format and content: *element_counts.txt tables show the number of counts for each elements based on the barcode_element_association_table.txt
Library strategy: Massively Parallel Reporter Assay

growth_protocol: HepG2 cells were grown in DMEM with high glucose and 10% FBS.

extract_protocol:
We produced lentivirus in 293FT cells using established protocols and filtered media (0.45 uM) to obtain virus. We seeded HepG2 cells in 6-well plates (1 million cells per well), and 24 hours post-seeding spinfected virus into HepG2 cells using established protocols (2000 RPM, 1.5 hours). After 48 hours incubation, we extracted RNA and DNA from cells using Norgen Total RNA purification kit and Qiagen DNeasy Blood & Tissue kit, respectively; we purified three replicates, using 8 wells per replicate (16 RNA columns per replicate).
Lentiviral MPRA data was produced by following the protocol in Gordon et al 2020 (PMID 32641802), with minor modifications. Oligos (n=138,420, Supplemental Table 6) were synthesized by Twist Bioscience, and were composed of 170 nucleotides test element with 15 nucleotides 5' flanking sequence and 15 nucleotides 3' flanking sequence (Supp Table X). First-round amplification of the oligo library was performed as described with 5BC-AG-f01 and 5BC-AG-r01, but a separate first-round amplification was performed in parallel with custom primers 5BC-AG-f01B (5'-CTCACTCAGCCTGCATTTCTGCCAGGGCCCGCTCTAGACCTGCAGGTCGGTTCACGCAATG-3') and 5BC-AG-r01B (5'- GCTTTCGCTTAGCGATGTGTTCACTTTGCACAGTACCGGATTGCCAAGCTGGAAGTCGAGCTTCCATTATATACCCTCTAGTGAGGACCGGATCAACT-3'). These two reactions gave one library with test elements in forward orientation and one library with test elements in reverse orientation. These libraries were combined in equal quantities before second-round PCR amplification. For barcode association sequencing, we modified the read 1 and read 2 sequencing primers for our dual orientation library to (read 1) 5'- CTGCATTTCTGCCAGGGCCCGCTCTAGACCTGCAGG-3' and (read 2) 5'- TGGAAGTCGAGCTTCCATTATATACCCTCTAGTG-3'. All other primers and protocol steps followed the published method.
Lentiviral MPRA as described in PMID 32641802


title: Tag7E11_Tag01

tag: strain


title: Tag7E1_Tag01


title: HepG2 cells, DNA_Rep3


title: ND3

description: active pinching replicate 3

tag: genotype

value: active asexual repro.


title: Tag7D9_Tag01


title: 1-TI2-A002

tag: diagnosis


title: HepG2 cells, DNA_Rep2


title: ND2

description: active pinching replicate 2


title: HepG2 cells, DNA_Rep1


title: Tag7D8_Tag01


title: 19-TI2-A013


title: ND1

description: active pinching replicate 1


title: Tag7D7_Tag01


title: 17-TI2-A012


title: HepG2 cells, Association_Sequencing

description: Plasmid DNA library

library_source: other

molecule: other


title: HepG2 cells, RNA_Rep2


title: Tag7D6_Tag01


title: Tag7D5_Tag01


title: 16-TI1-A011


title: FR2_NK_rep3 RNA-seq

first: fanyi

last: meng

address: haidian distinct

institute: peking university

data_processing:
Data filtering The raw data obtained by sequencing was filtered using SOAPnuke (v1.5.6)
Differential gene analysis Use HISAT2 (v2.1.0) software to compare the clean data to the reference genome.
Use Bowtie2 (v2.3.4.3) to align the clena data to the reference gene set.
RSEM (v1.3.1) software was used to quantify gene expression, and pheatmap (v1.0.8) was used to draw a cluster heat map of gene expression in different samples.
DESeq2 (v1.4.5) was used for differential gene detection, and the condition was Q value≤0.05 or FDR≤0.001.
Assembly: GCF_000001405.39_GRCh38.p13

source_name: YT

extract_protocol:
Total RNA samples isolated from CTRL/hnCD16/FR1/FR2 YT cells were treated with DNase using a column assay. High-quality RNA (280/260 and 230/260 both over 1.7, RIN/RQN>9) was subjected to ribosomal RNA depletion followed by library construction.
Sample testing: According to the sample and product requirements, select the corresponding testing method for quality inspection. mRNA isolation: A certain amount of RNA sample was taken, denatured at a suitable temperature to open its secondary structure, and mRNA was enriched using oligo(dT) magnetic beads. mRNA interruption: Add an interruption reagent to the mRNA obtained in the previous step, react at an appropriate temperature for a certain period of time, and fragment the mRNA. cDNA synthesis: Prepare the first-strand synthesis reaction system and set the reaction program to synthesize the first-strand cDNA; prepare the second-strand synthesis reaction system and set the reaction program to synthesize the second-strand cDNA. Prepare the reaction system for end repair, add "A" and adapter ligation, and set the reaction program to repair the double-stranded cDNA end, and add A base at the 3' end; prepare the adapter ligation reaction system, and set the reaction program to make the adapter Ligated with cDNA. PCR Prepare a PCR reaction system and set up a reaction program to amplify the product. Library detection: Select the corresponding detection method according to the product requirements to check the quality of the library. Circularization: After denaturing the PCR product into a single strand, prepare a circularization reaction system and set up a reaction program to obtain a single-stranded circular product and digest the uncircularized linear DNA molecules. On-machine sequencing: The single-stranded circular DNA molecule is replicated by rolling circle to form a DNA nanoball (DNB) containing multiple copies. The obtained DNBs are added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced by combined probe-anchored aggregation technology (cPAS).

value: YT

value: natural-killer-like (NK-like) lymphoid cells

value: FR2 expressing

tag: treatment

value: lentiviral vector infection


title: FR2_NK_rep2 RNA-seq


title: FR2_NK_rep1 RNA-seq


title: 13-TI2-A009


title: Tag7D4_Tag01

value: CD11b+ cells


title: 10-TI1-A007


title: Crisp_3

city: Chongqing

first: wei

middle: Sheng

address: xinqiao street

department: gastroenterology

institute: Xinqiao hospital

data_processing:
Fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)])
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Genome_build: GRCh38
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample

source_name: MGC803 cells

growth_protocol: MGC803 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37 °C in 5% CO2

extract_protocol:
The culture medium was removed and cells were washed twice with PBS. Then, RNA was isolated using Trizol reagent. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: MGC803 cells

value: Gastric adenocarcinoma cells

value: FOXM1 knockout


title: FR1_NK_rep2 RNA-seq

value: FR1 expressing


title: Tag7D12_Tag01


title: Tag7D11_Tag01


title: Non-DEN, WT replicate 1, Multiome snATACseq

city: La jolla

first: Chiara

last: Nicoletti

state: CA

address: 10901 North Torrey Pines Road

department: Development, Aging and Regeneration Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Reads were then aligned to the mouse genome mm10/GRCm38 using CellRanger (v3.1.0). Doublets presence for each replicate was inferred with Scrublet (v0.2.1) (Wolock et al., 2019) within Python (v3.8). Filtered barcode and count matrices produced by CellRanger were used for downstream analyses in R (v3.6.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tibialis anterior and gastrocnemius

extract_protocol: Samples were processed as previously described in (Liu et al., 2015), and sorted by fluorescence activated cell sorting (FACS) to remove cell debris, doublets and dead cells. 100,000 live cells/sample were sorted and used for downstream processing with the 10X Genomics 3’ v3 kit for single-cell gene expression. 12,000 cells were used for library preparation, a little over the 10,000 suggested by the 10X protocol, in order to reach a higher capture rate. Libraries were constructed per manufacturer’s instructions and sequenced using Illumina’s NextSeq platform.

treatment_protocol: For each time-point post denervation (namely, 2, 5 and 15 days p.d., as well as the non-denervated control (abbreviated as Non-DEN in all figures and tables), 1 wild-type male C5Bl6/N mice at 3 months of age was used for each of the two biological replicates. After sciatic nerve transection, we collected two muscles downstream to the sciatic nerve, the tibialis anterior (TA) and gastrocnemius (GA) muscles.

value: Skeletal muscle-residents cells

value: Tibialis anterior and gastrocnemius

value: 12 weeks old


title: 23-55-GC

city: College Station

first: Destiny

middle: A

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

description:
mice-count.csv
mice-count-normalized.csv

data_processing:
Sequence reads were mapped to GRCm38.94 using STAR version 2.6.0a
Read count extraction was performed using HTSeq version 0.12.3
Read normalization was performed using edgeR.
Assembly: GRCm38.94
Supplementary files format and content: tab-deliminated csv file includes raw counts for each sample
Supplementary files format and content: tab-deliminated csv file includes normalized counts for each sample

source_name: primary colonocyte

growth_protocol: All experiments utilizing mice were approved and conducted in rigorous accordance with the Texas A&M University Institutional Animal Care and Use Committee (protocol number) and conformed to NIH guidelines. To generate a conditional colonic-targeted mutant APC mouse model (Figure 2), CDX2P-CreERT2 mice (IMSR Cat# JAX_022390, RRID:IMSR_JAX:022390) were crossed with Lgr5-EGFP-IRES-CreERT2-APCloxP/+ mice145. Mice were housed in cages in a temperature- and humidity-controlled animal facility with a 12 h light/dark cycle and fed standard chow.  For all in vivo experiments, mice were weaned at 3 weeks of age, acclimated and fed a semi-purified modified AIN-76A rodent diet with 10% (w/w) safflower oil, 21% casein, 43% sucrose, 16% cornstarch, 5% Solka Floc FCC200 (cellulose), 3.7% AIN-76 mineral mix, 0.1% AIN-76 vitamin mix, 0.3% methionine and 0.2% choline bitartrate (Research Diets Inc, D03092902) for 2 wks prior to induction of oncogenic APC580D in the colon by injection of tamoxifen. Mice were provided with fresh diet every three days. All animals had access to food and water at all times. To induce oncogenic APC580D, mice (minimum 8 weeks of age) were intraperitoneally injected once per day for four consecutive days with 100 mg/kg tamoxifen (Sigma-Aldrich, T5648) dissolved in corn oil (carrier), fed diet and weighted every single day until termination. Mice were terminated by CO2 asphyxiation followed by cervical dislocation at the times indicated in each study.

extract_protocol:
AfGC (Apc 850/850), AGC (Apc 850/+) and GC (Apc+/+) mice, were fed a 5% corn oil diet, 2 weeks prior to colonic induction of oncogenic Apc by injection of tamoxifen (100 mg/kg, four times) and termination after 3 (AfGC and GC) or 10 (AGC) weeks (n=4 per group). RNA from cells lines and mouse colonic crypts was extracted using a RNAeasy Micro Kit (Qiagen) followed by DNase treatment using an DNA-free DNA Removal Kit (Invitrogen) in accordance with the manufacturer’s protocol. RNA quality was assessed using an Agilent Bioanalyzer (Agilent Technologies). Only samples with an RNA quality of RIN≥8 were used. RNA concentration was measured using spectrophotometry.
Libraries were constructed usingthe Illumina Stranded mRNA Prep kits following manufacturer's instructions using 100 ng total RNA.

value: primary colonocyte

value: epithelial

value: APC +/+


title: 22-79-GC


title: 24-8-AGC


title: 19-40-AGC

value: APC -/+


title: HepG2 cells, RNA_Rep3


title: Crisp_1


title: Tag7D10_Tag01


title: WT_3

value: untreated


title: hnCD16_NK_rep2 RNA-seq

value: YT

value: hnCD16 expressing


title: FR1_NK_rep3 RNA-seq

value: natural-killer-like (NK-like) lymphoid cells


title: 18-42-GC


title: Tag7D1_Tag01


title: Tag7D2_Tag01


title: WT_2


title: 17-67-GC


title: hnCD16_NK_rep1 RNA-seq

value: lentiviral vector infection


title: Tag7C9_Tag01

value: CD11b+ cells


title: Crisp_2

value: MGC803 cells


title: 21-17-AfGC

value: APC -/-


title: Control_NK_rep3 RNA-seq

value: eGFP control expressing


title: FR1_NK_rep1 RNA-seq

value: FR1 expressing


title: 16-27-AGC


title: WT_1

value: Gastric adenocarcinoma cells


title: RNF112_3

value: infected with RNF112 virus


title: hnCD16_NK_rep3 RNA-seq


title: RNF112_2


title: 15-105-AGC


title: Tag7C6_Tag01


title: Control_NK_rep2 RNA-seq


title: RNF112_1


title: 13-89-AfGC


title: Tag7C8_Tag01


title: 14-34-GC


title: Control_NK_rep1 RNA-seq


title: 4-cells,rbpms2 morpholino,rep3

city: Nanjing City

first: Cheng

last: Zhou

address: Hanzhong Road no.140

institute: Nanjing Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
① Removing reads containing sequencing adapter; ② Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; ③ Removing reads whose unknown base ('N' base) ratio is more than 5%, then clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to GRCM39/mm39 using HISAT2 (v2.0.4)
Thereafter, Ericscript (v0.5.5) and rMATS (V3.2.5)were used to fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，after that expression level of gene was calculated by RSEM (v1.2.12)
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: embryos

extract_protocol:
RNA was harvested using phenol-chloroform extraction
Follow Tagmentation-based library construction protocol. PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. DNA was quantified by Agilent Technologies 2100 bioanalyzer.

value: embryos

value: rbpms2 knockdown

value: rbpms2 morpholino injected


title: Tag7C4_Tag01


title: Con_3

value: infected with control virus


title: 12-16-GC

value: primary colonocyte

value: epithelial

value: APC +/+


title: Tag7C3_Tag01


title: 4-cells,rbpms2 morpholino,rep2


title: 11-73-GC


title: 4-cells,rbpms2 morpholino,rep1


title: Con_2


title: Tag7C2_Tag01


title: 10-70-AfGC


title: 4-cells,non-silencing morpholino,rep3

value: control

value: non-silencing morpholino injected


title: Tag7C12_Tag01


title: Con_1


title: SubjectID 5015004, LS skin, W16

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description: column "sam117" in counts.matrix

data_processing:
Libraries prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina Nova 6000 with pair-end 100 cycles. Our sequencing depth ranged 50M reads, Image analysis and bases calling was conducted in real-time by the lllumina analysis pipeline.
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Genome_build: GRCh37
Supplementary_files_format_and_content: counts.matrix (tab delimited gene expression data of each sample)

source_name: Skin

extract_protocol: Total RNA was extracted from skin biopsies by the Qiagen miRNeasy Mini Kit (Valencia, CA, USA). DNA was removed with on-column DNase digestion by the Qiagen RNase-free DNase Set. The RNA yield and quality were determined with NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA),

tag: condition

value: psoriatic plaques

tag: individual

value: Secukinumab

tag: timepoint

value: LS


title: 4-cells,non-silencing morpholino,rep2


title: 09-403-GC

tag: cell line


title: SubjectID 5015004, NL skin, BL

description: column "sam115" in counts.matrix

value: BL

value: NL


title: 08-118-AGC

value: APC -/+


title: SubjectID 5015004, LS skin, BL

description: column "sam116" in counts.matrix


title: 4-cells,non-silencing morpholino,rep1


title: Tag7C10_Tag01

value: CD11b+ cells


title: Tag7C11_Tag01


title: 07-7AfGC

value: APC -/-


title: Tag7C5_Tag01


title: SubjectID 5015003, LS skin, W16

description: column "sam114" in counts.matrix


title: 06-109-AGC


title: Tag7B9_Tag01


title: Placenta, Male, Control, rep4 [C2R2]

city: Detroit

first: Gil

last: Mor

address: 275 E. Hancock

institute: Wayne State University School of Medicine

data_processing:
Base calling was conducted using HiSeq Control Software (placenta) or NovaSeq Control Software (decidua), converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36 (Placenta) or BBDUK from BBMap package v.38.90 (Decidua)
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR aligner v.2.5.2b
Read count extraction was performed using Subread package v.1.5.2 (Placenta) or HTSeq-count v.2.0.1 (Decidua)
Read count normalization was performed using DESeq2 package (Placenta) or edgeR (Decidua)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Placenta

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for Placental RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols. RNA libraries for Decidua RNA-seq were prepared using Lexogen QuantSeq 3' mRNA-Seq FWD with UDI 12 nt (Unique Dual Indexing) kit according to manufacturer's protocols.

treatment_protocol: C57B/l6 mice were exposed to 50ppm benzene for 5 hours a day from E0.5 to E17.5. Tissues were collected on E17.5

value: Placenta

tag: Sex

value: Male

value: Control

tag: mother


title: Placenta, Female, Control, rep4 [C2R3]

value: Female


title: Tag7C1_Tag01

tag: age


title: SubjectID 5015003, LS skin, BL

description: column "sam113" in counts.matrix


title: 05-223-AGC

value: primary colonocyte


title: Tag7B8_Tag01


title: Placenta, Female, Control, rep3 [C2R1]


title: 04-624-GC

value: epithelial


title: SubjectID 5015003, NL skin, BL

description: column "sam112" in counts.matrix


title: Placenta, Male, Control, rep3 [C2L3]


title: SubjectID 5015002, LS skin, W16

description: column "sam111" in counts.matrix


title: 03-419-GC

value: APC +/+


title: Placenta, Female, Control, rep2 [C1R3]


title: Tag7B6_Tag01


title: Tag7B5_Tag01


title: SubjectID 5015002, LS skin, BL

description: column "sam110" in counts.matrix


title: 02-18-AGC


title: SubjectID 5015002, NL skin, BL

description: column "sam109" in counts.matrix


title: Placenta, Male, Control, rep2 [C1R1]


title: IMCE_Bcat_3

description:
cell_culture-count.csv
cell_culture-count-normalized.csv

source_name: IMCE Bcat

growth_protocol: Conditionally immortalized young adult mouse colonic epithelium (YAMC), Immortomouse × MIN colonic epithelium (IMCE) and IMCE β-catenin (IMCE βcat)  isogenic cell lines were seeded, incubated with RPMI-1640 media (ThermoFisher, 21870076) supplemented with 1% GlutaMAX-I (ThermoFisher, 35050061), 5% Fetal Bovine Serum (FBS) (HyClone, SH30070.03), 0.1% ITS Premix Universal Culture Supplement (Corning, 354351), 1% Penicillin-Streptomycin (PenStrep) (ThermoFisher, 15140148) and 10% IFN-γ (Sigma, 11276905001) (IFN-γ was added freshly to media immediately prior to use) (complete mouse RPMI-1640) under permissive conditions, 33° C with 5% CO2, and grown to 70-90% confluency after 48 h. YAMC, IMCE and IMCE βcat cell lines were authenticated by STR profiling and an interspecies contamination test (CellCheck) performed at IDEXX BioResearch. All cell lines employed in our experiments tested negative for mycoplasma bacteria as assessed by a universal mycoplasma detection kit (30-1012K; American Type Culture Collection, Manassas (ATCC), VA).

extract_protocol:
YAMC (Apc +/+), IMCE (Apc 850/-) and IMCE βcat (Apc 850/+ βcat-/+) cell lines were cultured until ~80% confluent. Three separate experiments were conducted for each cell line (n=3).
Libraries were constructed usingthe Illumina Stranded mRNA Prep kits following manufacturer's instructions using 250 ng total RNA.

value: IMCE Bcat

value: APC -/+Bcat -/+


title: Tag7B3_Tag01

extract_protocol:
18 days after LPC injection, mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; gray matter was isolated from the frontal cortex and white matter was isolated form optic tract, medial lemniscus and corpus callosum (attached gray matter and choroid plexus were carefully removed). Single cells were isolated using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D to a final concentration of 45 mM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. The dissociated cell suspension was passed through a 70 mm cell strainer before labeling. Subsequently, cells were blocked with mouse FcR-blocking reagent (CD16/CD32 Monoclonal Antibody) and then stained for with the antibodiy against CD11b (PE/Cy7,M1/70, eBioscience, Cat:48-0451-82,1:200) and afterwards washed with PBS (Sigma, D8537). Cells were then stained with DAPI (4’,6-diamidino-2-phenylindole, 1:10000 dilution; Sigma)  and viable (DAPI-negative) single CD11b-positive cells were sorted by flow cytometry (SH800; Sony) into 96 well plates filled with 4 mL lysis buffer containing 0.05% Triton X-100 (Sigma) and, ERCC spike-in Mix (1:24000000 dilution), 2.5 mM oligo-dT, 2.5 mM dNTP and 2 U/mL of recombinant RNase inhibitor (Clontech).
The 96-well plates containing the sorted single cells were thawed and incubated for 3 min at 72°C and thereafter immediately placed on ice. To perform reverse transcription (RT) we added into each well a master mix of 0.59 μL H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μL Recombinant RNase Inhibitor (Clontech), 2 μL Betaine (5 M Sigma), 0.5 μL DTT (100 mM) 0.06 μL MgCl2 (1 M Sigma), 0.1 μL Templateswitching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next RT reactions were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; ending with 70°C for 5 min for enzyme inactivation. Preamplification of cDNA was performed by adding 12.5 μL KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μL H2O, 0.25 μL ISPCR primers (10 μM, 5’ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μL Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 23 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure beads (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Libraries were assessed by Bio-analyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and quantified using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies). Further selection of samples was performed via qPCR assay against ubiquitin transcripts Ubb77 (primer 1 5’-GGAGAGTCCATCGTGGTTATTT-3’ primer 2 5’-ACCTCTAGGGTGATGGTCTT-3’, probe 5’-/5Cy5/TGCAGATCTTCGTGAAGACCTGAC/3IAbRQSp/-3’) measured on a LightCycler 480 Instrument II (Roche). Samples were normalized to 160 pg/μL. Sequencing libraries were constructed by using in-house produced Tn5 transposase. Libraries were barcoded, pooled and purified in 3 rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library. Libraries were then sequenced with 100 bp paired-end sequencing on DNBSeq platform (BGI group).


title: Placenta, Male, Control, rep1 [C1L3]


title: Tag7B4_Tag01


title: SubjectID 5015001, LS skin, W16

description: column "sam108" in counts.matrix

value: psoriatic plaques


title: IMCE_Bcat_2


title: Tag7B2_Tag01


title: Placenta, Female, Control, rep1 [C1L2]


title: SubjectID 5015001, LS skin, BL

description: column "sam107" in counts.matrix

value: Secukinumab


title: Placenta, Female, Benzene, rep4 [B7R4]

value: Benzene


title: SubjectID 5015001, NL skin, BL

description: column "sam106" in counts.matrix

value: BL


title: PD2

description: steady state replicate 2

value: physa

value: genome Putnam et al. (2007)

value: steady state


title: Tag7B12_Tag01

value: CD11b+ cells


title: IMCE_3

source_name: IMCE

value: IMCE

value: APC -/+


title: Placenta, Male, Benzene, rep4 [B7R2]

value: Placenta

value: Male


title: SubjectID 5009001, LS skin, BL

description: column "sam105" in counts.matrix

value: Guselkumab

value: LS


title: Tag7B11_Tag01


title: Placenta, Male, Benzene, rep3 [B7L2]


title: IMCE_2

value: epithelial


title: Tag7B10_Tag01


title: SubjectID 5009001, NL skin, BL

description: column "sam104" in counts.matrix

value: NL


title: IMCE_1


title: YAMC_3

source_name: YAMC

value: YAMC

value: APC +/+


title: Tag7B1_Tag01


title: Placenta, Female, Benzene, rep2 [B5R2]

value: Female


title: Placenta, Female, Benzene, rep3 [B7L1]

value: Benzene


title: SubjectID 5007001, LS skin, W16

description: column "sam103" in counts.matrix

value: psoriatic plaques


title: YAMC_2


title: Placenta, Male, Benzene, rep2 [B5R1]


title: IMCE_Bcat_1

value: IMCE Bcat

value: APC -/+Bcat -/+


title: YAMC_1


title: SubjectID 5007001, NL skin, BL

description: column "sam101" in counts.matrix

value: BL


title: 4T1-control tumor, alum treated, bio rep 6 [4T1-control_alum_6.2]

first: K Dane

last: Wittrup

state: MA

department: Biological Engineering, Chemical Engineering, Koch Institute of Integrative Cancer Research

institute: Massachusetts Institute of Technology

description:
75-nt kit
4T1-control_alum_6.2

data_processing:
Data preprocessing and count matrix construction were performed using the Smart-seq2 Multi-Sample v2.2.0 Pipeline (RRID:SCR_018920) on Terra
Assembly: GENCODE mouse (M21) reference genome
Supplementary files format and content: Metadata spreadsheet containing sample information
Supplementary files format and content: Count matrix containing counts each sample
Supplementary files format and content: Gene metadata spreadsheet

source_name: tumor

extract_protocol:
Total RNA was extracted using RNAeasy plus mini kit
RNA-sequencing was performed by the BioMicro Center at MIT using a modified version of the SCRB-seq protocol (https://www.biorxiv.org/content/10.1101/003236v1)

treatment_protocol: Balb/c mice were inoculated with 1e6 CT26 or 5e5 4T1, 4T1-CAT, or 4T1-control cells subcutaneously on their flank on day 0. 4T1-CAT and 4T1-control cells are 4T1 cells engineered to express catalase (CAT) and GFP or GFP alone respectively in a doxycyline (DOX) inducible fashion. On day 4, mice with 4T1-CAT or 4T1-control tumors were started on a DOX-containing diet to induce gene expression. On day 6, mice were treated intratumorally with 20 ug CAT-ABP + 100 ug alum or alum along. Tumors were harvested on day 8  and processed for RNA extraction.

value: tumor

value: alum

tag: technical replicate