title: c1c2_Dark_m6A_rep2

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

description: Dark treated cry1 cry2 m6A IP replicate 1

data_processing:
Adapters were removed from reads with the AdapterRemoval tool with adapter sequence 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'.
Reads were then mapped against the Arabidopsis (TAIR10) genome with STAR (v 2.5.3a).
Assembly: TAIR10
Supplementary files format and content: bigwig files were generated using deepTools; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP.
Library strategy: m6A-seq

organism: Arabidopsis thaliana

source_name: 6-day-old seedlings

growth_protocol: Seedlings were grown on 1/2-strength Murashige and Skoog (MS) medium (1/2 MS) with 0.8% sucrose under dark or continous blue light (30 μmol m-2 s-2) for 6 days at 21ºC ±2ºC.

extract_protocol:
Seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. mRNA was purified using OligodT beads. mRNA was fragmented and isolated with m6A antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. m6A-seq libraries were prepared using RNA Library Prep Kit (NEB, E7770). Libraries were sequenced on the Illumina Nova 6000 platform as single-end 150 bp reads.

value: 6-day-old seedlings

tag: rip antibody

value: cry1 cry2

value: dark


title: c1c2_Dark_m6A_rep1

status: Public on Mar 06 2023

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

tag: treatment


title: Mouse Liver HFD-SB1

type: RNA

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

description: Gene expression data from murine liver

hyb_protocol: Following fragmentation, 2.3 µg of single-stranded cDNA were hybridized for 16 hr at 45ºC on Clariom™ S Assay, Mouse chips. Chips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Command Console® 2.0 Technical Manual (Affymetrix).

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix AGCC software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis (ANOVA unpaired one-way) were performed using the TAC software (Transcriptome Analysis Console) developed by Affymetrix.

label: biotin

organism: Mus musculus

source_name: Mouse Liver HFD-SB1

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 50ng total RNA Labeling Protocol (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression ArraysWT Pico Reagent Kit, ©2015 Affymetrix Inc.)

growth_protocol: Fronzen liver was processed for RNA extraction.

extract_protocol: Total RNA was isolated from frozen tissues using the easy-blue total RNA Extraction kit (#17061, iNtRON Biotechnology, Inc., Seongnam, Korea)

treatment_protocol: Liver tissue was snap frozen after animal sacrifice.

value: Murine liver


title: c1c2_Dark_input_rep2

description: Dark treated cry1 cry2 input replicate 1


title: Mouse Liver HFD-SB3

description: Gene expression data from murine liver

source_name: Mouse Liver HFD-SB3


title: Mouse Liver HFD3

description: Gene expression data from murine liver

source_name: Mouse Liver HFD3


title: Mouse Liver HFD-SB2

description: Gene expression data from murine liver

source_name: Mouse Liver HFD-SB2


title: c1c2_Blue_m6A_rep1

description: Blue light treated cry1 cry2 m6A IP replicate 1

value: blue light


title: c1c2_Dark_input_rep1


title: c1c2_Blue_input_rep1

description: Blue light treated cry1 cry2 input replicate 1


title: Mouse Liver HFD1

description: Gene expression data from murine liver

source_name: Mouse Liver HFD1


title: c1c2_Blue_input_rep2


title: Mouse Liver STD-SB4

description: Gene expression data from murine liver

source_name: Mouse Liver STD-SB4


title: cry1_Dark_m6A_rep1

description: Dark treated cry1 m6A IP replicate 1


title: cry1_Dark_m6A_rep2

description: Dark treated cry1 m6A IP replicate 1


title: Mouse Liver STD-SB1

description: Gene expression data from murine liver

source_name: Mouse Liver STD-SB1


title: Mouse Liver STD-SB2

description: Gene expression data from murine liver

source_name: Mouse Liver STD-SB2


title: Mouse Liver STD-SB3

description: Gene expression data from murine liver

source_name: Mouse Liver STD-SB3


title: cry1_Dark_input_rep2

description: Dark treated cry1 input replicate 1


title: Mouse Liver HFD2

description: Gene expression data from murine liver

source_name: Mouse Liver HFD2


title: Mouse Liver STD4

description: Gene expression data from murine liver

source_name: Mouse Liver STD4


title: Input Crosslinked RMC2C-mCherry

city: Strasbourg

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1 with "--broad" parameter for H3K27ac and BRG1.  Peaks were called using MACS 1.4 for MYC and MAX.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney

growth_protocol: Fresh RMC2C bearing either SMARCB1 or mCHERRY were cultured for maximum 10 passages at a dilution of 1:2 in MEM + 10% FCS + AANE + PS + G418 (50uM).

extract_protocol:
Crosslinked ChIP was performed according standard protocols (see Strub et al, 2011). Native ChIP was performed according to standard protocols (see Wagschal et al., 2007).
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 0.7 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 3cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: Cells were treated with 2uM doxycyline for 48hrs.

value: Kidney

tag: cell line

tag: antibody

value: IgG (Abcam 171870)

tag: chip-seq condition

value: Crosslinked

tag: inducible transgene

value: mCherry


title: Mouse Liver STD3

description: Gene expression data from murine liver

source_name: Mouse Liver STD3


title: cry1_Dark_input_rep1

description: Dark treated cry1 input replicate 1


title: cry1_Blue_m6A_rep2

description: Blue light treated cry1 m6A IP replicate 1


title: Mouse Liver STD2

description: Gene expression data from murine liver

source_name: Mouse Liver STD2


title: Secondary Screen, Day 15, Biol rep 3

city: Boston

first: Nora

middle: E

last: Renthal

state: MA

address: 3 Blackfan Circle

department: Endocrinology

country: USA

institute: Boston Children's Hospital

data_processing:
Pooled Screening Deconvolution performed by the Broad Institute's Genetic Perturbation Platform using PoolQ.
PoolQ produces a matrix of read counts for sgRNA barcodes, from which we calculated Log fold change (LFC) values comparing the top 10% CD200 expressing cells with the bottom 10% CD200 expressing cells for each barcoded sgRNA.
Guide-level LFC is used as an input into the Broad's Hypergeometric Distribution Tool, which assigns sgRNA barcodes to their respective genes, and generates an average p-value and LFC for each gene.
Primary Screen meta-analyzed Z-scores were generated based on LFC values for replicates across both timepoints
Assembly: GRCm38 (.chip files are used to assign barcodes to genes - CP0044 for primary screen, CP1620 for secondary screen)
Supplementary files format and content: .xlsx spreadsheets containing sgRNA barcode counts from sequencing
Supplementary files format and content: .txt files containing output of Hypergeometric Analyses
Library strategy: DNA-Seq

growth_protocol: Growth plate like chondrocyte (GPLC) cells containing Cas9 and a genome-wide CRISPRko sgRNA library were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 100 U/mL Penicillin/ 100mg/mL Streptomycin,  50 ug/mL Ascorbic acid, and 1X Insulin/Transferrin/Selenium in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
gDNA was extracted from sorted cells using QIAGEN QIAamp DNA Blood Midi Kit and concentrations were quantified using the Qubit fluorometer.
Integrated construct barcode sequences were amplified by PCR and prepared using the AMPure purification system.

tag: time

value: Day 15


title: c1c2_Blue_m6A_rep2


title: Secondary Screen, Day 15, Biol rep 1 and 2

source_name: Growth plate like chondrocyte (GPLC) cells


title: Secondary Screen, Day 4, Biol rep 3

value: Growth plate like chondrocyte (GPLC) cells

value: Day 4


title: cry1_Blue_m6A_rep1


title: cry1_Blue_input_rep2

description: Blue light treated cry1 input replicate 1


title: cry1_Blue_input_rep1


title: Secondary Screen, Day 4, Biol rep 1 and 2


title: Primary Screen, Day 15, Biol rep 2


title: Primary Screen, Day 15, Biol rep 3


title: WT_Dark_m6A_rep2

description: Dark treated WT m6A IP replicate 1


title: WT_Dark_input_rep2

description: Dark treated WT input replicate 1


title: Primary Screen, Day 4, Biol rep 3


title: WT_Dark_input_rep1

description: Dark treated WT input replicate 1


title: Primary Screen, Day 15, Biol rep 1


title: WT_Blue_m6A_rep1

description: Blue light treated WT m6A IP replicate 1


title: Primary Screen, Day 4, Biol rep 1


title: WT_Blue_m6A_rep2


title: OB 608-4 [X11530]

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
Sequence reads were trimmed of adapter using cutadapt and trimmed and filtered for quality using FastX Toolkit
Trimmed reads were mapped to mm10 using hisat2
read count using htseq-count
data normalization and differential gene expression using deseq2
Assembly: mm10
Supplementary files format and content: tab delimited file containing deseq2 normalized read counts for each sample

molecule: polyA RNA

source_name: Brain

growth_protocol: OB and CT BCECs were isolated ex vivo after 3 days from weanling mice infected with La Crosse virus (2000PFU/mouse, intraperitoneal)  or mock inoculated (200ul/mouse)

extract_protocol:
RNA was harvested using RNA isolation kit (Zymo Research). 170ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Control: Mock inoculated mice
C57BL/6 weanling mice were infected with a 2000 PFU IP dose of LACV diluted into 200ul of sterile, pharmaceutical grade PBS. Mock mice received an equivalent volume of uninfected Vero supernatant diluted in PBS

value: Brain

tag: strain

tag: cell type

value: olfactory bulb BCECs

value: WT

value: LACV


title: WT_Blue_input_rep1

description: Blue light treated WT input replicate 1

source_name: 6-day-old seedlings


title: OB 608-1 [X11528]


title: Primary Screen, Day 4, Biol rep 2


title: Mouse Liver STD1

description: Gene expression data from murine liver

source_name: Mouse Liver STD1


title: WT_Blue_input_rep2

description: Blue light treated WT input replicate 1


title: OB 607-3 [X11527]

value: Mock


title: OB 608-2 [X11529]


title: OB 607-2 [X11526]


title: RXRa.1

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

data_processing:
Quality control was performed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/), adapter contaminants were trimmed using Trimmomatic (github.com/usadellab/Trimmomatic), reads were aligned to a custom-built reference genome (RXRα and GFP plasmid sequences were added to GENCODE GRCm38 genome) using hisat2 (daehwankimlab.github.io/hisat2/), duplicate reads were removed using Picard MarkDuplicate tool (broadinstitute.github.io/picard/), and finally count matrices were generated using the featureCounts function of the subread package (subread.sourceforge.net/featureCounts.html) and a comprehensive gene annotation file obtained from GENCODE (GRCm38 vM23). Reads mapping to the plasmid codon-optimized Rxra overexpression sequence were added to reads mapping to the endogenous Rxra sequence (ENSMUSG00000015846).
Assembly: GRCm38
Supplementary files format and content: RXRa_OE_countmatrix.txt is a text file containing the read counts for the bulk tissue RNA-seq. RXRa_D1D2_OE_countmatrix.txt is text file containing the read counts for the isolated D1 and D2 RNA-seq samples. Plasmid_RXRa_GFP_sequence.fa is a fasta file containing the sequences for RXRa and GFP that were added to the reference genome prior to read alignment.

source_name: Nucleus Accumbens

extract_protocol:
For bulk tissue RNAseq, RNA extraction was performed using the RNeasy Micro Kit (Qiagen) following manufacturer instructions. For cell-type-specific RNAseq, RNA was extracted from frozen TRIzol LS (Ambion) homogenates using the Direct-zol RNA Microprep Kit (Zymo Research) following manufacturer instructions.
For bulk tissue RNAseq, Sequencing libraries were prepared by Genewiz/Azenta with polyA selection and sequenced with Genewiz/Azenta on an Illumina HiSeq 4000 machine using a 2 × 150 bp pair-end read configuration to a minimum depth of 20 million reads per sample. For cell-type-specific RNAseq, ribo-depleted sequencing libraries were prepared with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa Biotech) following manufacturer instructions and sequenced with Genewiz/Azenta on an Illumina NovaSeq S4 machine using a 2 × 150 bp pair-end read configuration to a minimum depth of 40 million reads per sample.

treatment_protocol: Viral infusion in nucleus accumbens

value: Nucleus Accumbens

value: Bulk tissue

tag: gender

value: Male

tag: viral vector

value: HSV-RXRa-GFP

tag: rna extraction kit

value: RNeasy Micro Kit (Qiagen)


title: CTX 608-4 [X11524]

value: cortical BCECs


title: RXRa.4


title: RXRa.3


title: RXRa.2


title: OB 607-1 [X11525]


title: WT_Dark_m6A_rep1

description: Dark treated WT m6A IP replicate 1

value: 6-day-old seedlings

value: dark


title: CTX 608-2 [X11523]


title: GFP.4

value: HSV-GFP


title: GFP.3


title: CTX 607-2 [X11520]


title: GFP.2


title: CTX 607-3 [X11521]


title: GFP.1


title: CTX 608-1 [X11522]


title: CTX 607-1 [X11519]


title: CW606-3

growth_protocol: BCECs were isolated ex vivo after 3 hrs from mice treated with (retroorbital injection) vehicle or Poly I:C

extract_protocol:
100ug of Poly(I:C) (HMW) diluted in a 0.5mg/mL LyoVec transfection reagent solution (Invivogen) via a 100ul retroorbital (IV) injection
RNA was harvested using RNA isolation kit (Zymo Research). 115ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Controls: Vehicle Lyovec-treated mice

value: BCECs

value: Poly I:C-HMW/Lyovec (100ug/mouse)


title: CW606-2


title: CW606-1


title: ribo_WTS(-)_3

city: Kyoto

first: Masao

last: Doi

department: Department of Systems Biology

country: Japan

institute: Kyoto University, Graduate School of Pharmaceutical Sciences

data_processing:
Library strategy: Ribo-seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR v2.7.0
Alignment with STAR v2.7.0
Read quantitation using custom scripts
Genome_build: mm10
Supplementary_files_format_and_content: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

source_name: mouse embryonic fibroblasts

growth_protocol: Cells were grown in dish to full confluence before experiments.

extract_protocol:
RNase I footprinting, ribosome pelleting, RNA extraction
Cells were lysed with a lysis buffer containing cycloheximide. Following digestion of genomic DNA with DNase I, the lysate was centrifuged at 20,000 × g and the resultant supernatant was processed for library generation.
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for Ribo-seq) or TruSeq (illumina) (for mRNA-seq)

treatment_protocol: WTS (35°C -> 38.5°C) was applied 24-h after Dex synchronization. Otherwise the cells were kept at 35°C.

value: wild-type

value: mouse embryonic fibroblasts

value: WTS-


title: ribo_WTS(+)_3

value: WTS+


title: ribo_WTS(+)_2


title: CW605-3

value: Brain

value: WT

value: Lyovec (100ug/mouse)


title: CW605-2


title: rna_WTS(+)_2

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR v2.7.0
Alignment with STAR v2.7.0
Read quantitation using custom scripts
Genome_build: mm10
Supplementary_files_format_and_content: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

extract_protocol:
TruSeq Stranded Total RNA Library Prep Gold
Cells were lysed with a lysis buffer containing cycloheximide. Following digestion of genomic DNA with DNase I, the lysate was centrifuged at 20,000 × g and the resultant supernatant was processed for library generation.
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for Ribo-seq) or TruSeq (illumina) (for mRNA-seq)


title: CW575-3


title: rna_WTS(+)_1


title: CW605-1


title: rna_WTS(-)_3


title: CW575-1


title: rna_WTS(-)_1


title: CW574-4


title: rna_WTS(-)_2


title: ribo_WTS(-)_2


title: PCOS3

city: Shijiazhuang

first: Xiuhua

last: Xu

address: 215 Heping Road West

institute: Second Hospital of Hebei Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tissue

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 RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: tissue

value: endometrium

value: PCOS

value: secretory phase  secretory phase  secretory phase

value: no


title: CW574-3


title: CW574-1


title: PCOS1


title: OVULATE3

value: OVULATE


title: TCDD CD44loCD8+_2

city: Rochester

first: Christina

middle: Marie

last: Post

address: 601 Elmwood Ave, Box EHSC

department: Environmental Medicine

institute: University of Rochester School of Medicine & Dentristry

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--twopassMode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outReadsUnmapped Fastx"
READ COUNTING- htseq-count 0.6.1 with a GTF annotation file (Gencode M6): "-q -f bam -s no -r pos -i gene_name"
DIFFERENTIAL EXPRESSION ANALYSIS- DESeq2-1.12.4 with a p-value threshold of 0.05 within R version 3.3.2
Assembly: GENOME BUILD- GRCm38.p4 + Gencode-M6 Annotation
Supplementary files format and content: tab-delimited text file includes raw count values for each sample

source_name: Mediastinal lymph node

extract_protocol:
Mediastinal lymph nodes (MLNs) were harvested from female offspring on day 9 post-IAV infection. Single cell suspensions of MLN cells were stained with fluorochrome-conjugated antibodies against CD3, CD8, and CD44, then immediately sorted into CD3negCD4negCD8+CD44lo and CD3negCD4negCD8+CD44hi fractions using a BD FACS Aria II cell sorter (San Jose, CA).
One ng of total RNA was pre-amplified with the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Fluorometer (Life Technologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). cDNA (1 ng) was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane. Single end reads of 100 nucleotides were generated for each sample using Illumina's HiSeq2500v4.

treatment_protocol: Impregnated and lactating dams were gavaged with vehicle (peanut oil) or 1ug 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)/kg body weight on gestational day 0, 7, 14, and post natal day 2.  Female offspring were aged to maturity (6-10 weeks old) then infected with 120 HAU Influenza A virus (HKx31).

value: Mediastinal lymph node

tag: cell subtype

value: CD8+ T cells

value: TCDD


title: TCDD CD44hiCD8+_2


title: OVULATE2


title: VEH CD44loCD8+_2

value: VEH


title: OVULATE1


title: rna_WTS(+)_3

value: wild-type


title: TCDD CD44loCD8+_1


title: TCDD CD44hiCD8+_1


title: CW575-2

value: BCECs

value: Poly I:C-HMW/Lyovec (100ug/mouse)


title: VEH CD44loCD8+_1


title: VEH CD44hiCD8+_1


title: nTERT OE 2

city: London

first: Lou

last: Metherell

address: JVSC, QMUL, Charterhouse Square

department: Centre for Endocrinology

country: United Kingdom

institute: William Harvey Research Institute

description: 2 x 150bp paired-end sequence reads

data_processing:
FastQC Reads Quality Control version 3.0.1 (28/10/2020)
HISAT2 version 1.03 (1/6/2017)
subread_featureCounts version 0.1.0 (21/3/2019)
DESeq2 (11/12/2017)
Assembly: GRCh38
Supplementary files format and content: txt files: individual txt files for each sample containing the output data generated from FeatureCounts software, displaying the counts and gene length for each individual gene.
Supplementary files format and content: TPM.xlsx: TPM values for each gene for each sample were calculated and then combined into a single spreadsheet with samples in columns and genes in rows.

source_name: Skin

extract_protocol:
RNA was extracted using the QIAGEN RNeasy kits following manufacturer's protocol. RNA was quantified using a Nanodrop spectophotometer
Library construction was performed by Eurofins Genomics under their NGSelect RNA on Illumina. The library construction involved purification of poly-A containing mRNA molecules, mRNA fragmentation, random pried cDNA synthesis, adaptor ligation and adapter specific PCR amplification.

treatment_protocol: No treatment

value: Skin

value: N/TERT

value: Epidermal Keratinocyte

value: SGPl1 OE


title: nTERT OE 3

description: 2 x 150bp paired-end sequence reads


title: nTERT KO 3

description: 2 x 150bp paired-end sequence reads

value: SGPL1 KO


title: nTERT KO 2

description: 2 x 150bp paired-end sequence reads


title: PCOS2

value: tissue

value: endometrium


title: nTERT Control 3

description: 2 x 150bp paired-end sequence reads

value: WT


title: nTERT KO 1

description: 2 x 150bp paired-end sequence reads


title: SG4_ChIP_input_BiorepB

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

data_processing:
Sequenced libraries were Quality Checked (FastQC) and trimmed from Illumina sequencing adaptors by cutadapt (cutadapt -q 20 -O 3 -a CTGTCTCTTATACACATCT). Resulting reads were aligned to the human genome (hg38) using BWA-MEM. The alignments bam files were de-duplicated (picard MarkDuplicates) and used for generating genome tracks of G4 signal normalized to total library size (reads per million, RPM) for visual inspection.
Local enrichments were identified calling peaks with MACS2 (options: -q 0.01 --keep-dup all ) on the de-duplicated bam and the relative input library. G4 consensus regions of each biological replicate were obtained as the regions observed in 2 out of the 3 technical replicates (multiIntersectBed; using bedtools). The final cell-type consensus were defined as the regions reproducibly observed in 2 of the 3 biological replicates. The cell-type consensus was then compared to the OQs (20) and to accessible sites (12).
Assembly: hg38
Supplementary files format and content: bigWig (bw), narrowPeak (except for Input sample)
Supplementary files format and content: multi2.bed (consesus=overlapping regions across 2 of the 3 replicates)

growth_protocol: K562 cells (ATCC, CCL0243)  were cultured in RPMI 1640 (Thermo Fisher, 21875-034) supplemented with 10% of fetal bovine serum (FBS; Thermo Fisher, A3840402). U2OS cells (ATCC, HTB-96) were cultured in DMEM (Thermo Fisher, 41966-029) supplemented with 10% of FBS. Both cell lines were incubated at 37°C in 5% CO2.   K562 and U2OS cells were profiled by SG11-ChIP-seq.

extract_protocol:
Cell nuclei were extracted and sonicated. G4 containing DNA  was isolated with SG4 antibody.  For SG4 ChIP libraries, DNA was tagmented and the library was prepared using Nextera library preparation kit (20034197) by following the manufacturer instruction. The library was amplified using Nextera index primers (Illumina, FC-121-1030). Nanobody purification protocol: BL21 (DE3) E. coli chemically competent cells were transformed with pHEN2 plasmid carrying SG4 wild type sequence. Single colonies were inoculated in Terrific Broth medium the addition of 1% glucose and 100 μg/ml ampicillin. After overnight incubation, the starting culture were transferred into Terrific Broth medium containing 0.1% glucose and 100 μg/ml ampicillin, incubated at 37 °C until bacterial OD600 reached a value in the range of 0.6-0.8. After that, bacteria were induced with 0.5 mM IPTG for ~16 h at 28 °C. Bacterial lysed fraction containing the nanobody was loaded on Proteus 1-step batch Midi Spin columns (Generon) with Nickel resin (Sigma), and incubated at 4 °C for 1 hour, then the nanobo
Pulled-down DNA was tagmented using Illumina Tagment DNA TDE1 Enzyme and Buffer Kit following manifacturers' protocol. The libraries were prepared using Nextera XT Index Kit, amplified wuth NEB Next High Fidelity 2x PCR Master Mix, and cleaned up using Qiagen MinElute Reaction Cleanup Kit.

tag: chip antibody

value: input library


title: pmito

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

description: mitochondrial RNA sequencing data

data_processing:
For meccRNA prediction, identified the candidates with find_circ (Memczak et al., 2013)  and the junction reads were calculated as Reads Per Million (RPM)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: paratumor

extract_protocol:
The isolated mitochondria were homogenized in TRizol reagent (Life Technologies) by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: paratumor

tag: patient diagnosis

value: Hepatocellular Carcinoma

value: mitochondria


title: cmito

institute: University of Science and Technology of China

description: mitochondrial RNA sequencing data

source_name: tumor

value: tumor


title: nTERT Control 1

description: 2 x 150bp paired-end sequence reads


title: nTERT Control 2

description: 2 x 150bp paired-end sequence reads


title: SG4_ChIP_input_BiorepC


title: ChIP-seq_TEAD1_mut

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

data_processing:
mapping with Bowtie2 (version 2.3.4.1)
mapping with Bowtie2 (version 2.3.4.1)
Genome_build: hg19 from UCSC
Supplementary_files_format_and_content: bw and csv files were generated with featureCounts (version 2.0.1)

source_name: heart

growth_protocol: All the animal experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines for animal experiments of the University of Tokyo (Approved Number P17-058). All mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 12-h light/dark cycle with ad libitum access to food and water.

extract_protocol:
ChIP-seq samples (whole genome DNA) from 5×10^4 iPSCMs were extracted using the CUT&RUN assay kit (#86652, Cell Signaling Technology).
KAPA HyperPlus Library Preparation Kit（Kapa Biosystems, #KK8510）

treatment_protocol: Lmna Q353R knock-in mice were generated as previously described (Hara, S. et al. Generation of mutant mice via the CRISPR/Cas9 system using FokI-dCas9. Sci. Rep. 5, 1–9 (2015).)

value: iPS cardiomyocyte

tag: mutation

tag: name in supplementary file


title: SG4_ChIP_BiorepC_rep3


title: ChIP-seq_TEAD1_WT


title: SG4_ChIP_input_BiorepA


title: SG4_ChIP_BiorepC_rep2


title: ChIP-seq_H3K4me4_WT


title: SG4_ChIP_BiorepC_rep1


title: VEH CD44hiCD8+_2

tag: tissue

value: Mediastinal lymph node

value: CD8+ T cells

value: VEH


title: nTERT OE 1

description: 2 x 150bp paired-end sequence reads

value: Skin

tag: genotype


title: ChIP-seq_H3K4me3_mut


title: BmVasa-CLIP_SpnE-KD_rep2

first: Yurika

last: Namba

state: --- Select a state ---

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences, Graduate School of Science

data_processing:
BmVasa FAST-iCLIP: After removal of 3′ adaptor sequences by Cutadapt (version 4.0) (Martin 2015), reads shorter than 27 nt were discarded. PCR duplicates were removed by collapsing all identical reads containing the same random barcode at the 5′-end using fastx-collapser in FASTX-Toolkit (version 0.0.14) (http://hannonlab.cshl.edu/fastx_toolkit/index.html); then, the 5′ random barcode was removed from the reads. The reads were mapped against the Bombyx mori genome assembly (Nov. 2016) from the SilkBase database using STAR (version 2.7.9a) (Dobin et al. 2013) in random and multiple counting modes allowing up to 4% mismatches relative to read length. Genome-mapped reads were remapped against the silkworm gene library (see “Gene classification” section) using Bowtie (version 1.3.1) (Langmead et al. 2009) in random and multiple counting modes allowing up to two mismatches. Gene-mapped reads from the FAST-iCLIP data were processed using SAMtools (version 1.15) (Li et al. 2009). The reads mapped to the sense direction were normalized against the number of genome-mapped reads to RPM or RPKM with the addition of a pseudo-count for log transformation and FC calculation. Owing to the high correlation of replicate samples, the two replicate reads were merged for further analysis.
Assembly: the Bombyx mori genome assembly (Nov 2016) (Kawamoto et al. 2019) from the SilkBase database
Supplementary files format and content: BmVasa FAST-iCLIP: Tab-separated text files include normalized count of reads (RPM or RPKM) mapped to the silkworm gene library in sense direction.

organism: Bombyx mori

source_name: ovary

growth_protocol: BmN4 cells were cultured at 26°C in EX-CELL 420 serum-free medium for insect cells (Sigma-Aldrich) supplemented with 10% fetal bovine serum (Gibco) and 1× penicillin-streptomycin-glutamine (Thermo Fisher Scientific).

extract_protocol:
BmVasa FAST-iCLIP: FAST-iCLIP (Flynn et al. 2015) basically uses the standard iCLIP protocol (König et al. 2010) except that pulldown is performed in the step of cDNA purification using a 3'-end biotin-blocked adaptor and streptavidin beads in place of size selection by gel electrophoresis. BmN4 cells in the two 100-mm dishes treated with Luc (control) or Spn-E siRNA were used. BmN4 cells were washed once with ice-cold PBS and UV crosslinking was performed with irradiance of 200 mJ/cm^2 at 254 nm. The cells were subjected to immunoprecipitation using anti-BmVasa antibody (1C3D10) (Nishida et al. 2015). The beads were washed three times with wash buffer [30 mM HEPES-KOH (pH 7.3), 150 mM potassium acetate, 5 mM magnesium acetate, 5 mM dithiothreitol, 0.1% (w/v) NP-40, 2 μg/mL pepstatin, 2 μg/mL leupeptin, and 0.5% aprotinin], followed by partial RNA digestion with 1 U/μL RNase T1 for 15 min at room temperature. Then, the beads were washed three times with high-salt wash buffer [30 mM HEPES-KOH (pH 7.3), 150 mM potassium acetate, 5 mM magnesium acetate, 500 mM NaCl, 5 mM dithiothreitol, 0.1% (w/v) NP-40, 2 μg/mL pepstatin, 2 μg/mL leupeptin, and 0.5% aprotinin]. 3'-end RNA dephosphorylation was performed with T4 polynucleotide kinase and the 3'-ends of the RNAs were ligated to a radioactively labeled and preadenylated RNA adaptor using T4 RNA ligase 2, truncated KQ (New England Biolabs). The samples were analyzed by NuPAGE (Life Technologies) and RNA-protein complexes were transferred to nitrocellulose membranes. The RNA-protein complexes on nitrocellulose membranes were treated with proteinase K.
BmVasa FAST-iCLIP: Extracted RNAs were subjected to reverse transcription using SuperScript III Reverse Transcriptase (Life Technologies), followed by RNA degradation using RNaseA (Roche) and RNaseH (NEB). cDNA purification and cDNA circularization were performed by pulldown using Pierce Streptavidin Magnetic Beads (Life Technologies) and CircLigase II ssDNA Ligase (Epicentre). Libraries were then amplified with Q5 DNA polymerase and size-selected by gel electrophoresis. The libraries were sequenced on the MiSeq platform (Illumina) to obtain 51 nt single-end reads, resulting in 7,221,225 and 6,129,038 reads for Luc KD and 7,025,416 and 5,763,089 reads for Spn-E KD (Replicates 1 and 2, respectively).

treatment_protocol: BmN4 cells (0.5-1.5×10^6 cells) suspended in 100 μL of EP buffer [137 mM sodium chloride, 5 mM potassium chloride, 0.5 mM sodium hydrogen phosphate, and 2.1 mM HEPES-KOH (pH 7.1)] were transfected with 500-750 pmol siRNA duplex by electroporation with Nucleofector 2b (Lonza). Luciferase (Luc) siRNA was used as a control.

tag: cell line

value: ovary

value: Spn-E KD

tag: treatment

value: RNAi


title: BmVasa-CLIP_Luc-KD_rep1

value: Control (Luc KD)


title: SG4_ChIP_BiorepB_rep2


title: SG4_ChIP_BiorepB_rep1


title: BmVasa-CLIP_Luc-KD_rep2


title: BmVasa-CLIP_SpnE-KD_rep1


title: KFC L TN71

city: Orange

first: Patricia

middle: C

last: Lopes

state: CA

address: 450 N Center St

department: Biological Sciences

institute: Chapman University

data_processing:
Data filtering: reads containing adapters, reads containing N > 10% and low quality reads were filtered out
Mapping was done using HISAT2
HTSeq (v0.6.1) was used to count numbers of mapped reads.
Assembly: taeGut3.2.4, release 96, downloaded from Ensembl
Supplementary files format and content: tab-delimited text file includes raw (not normalized) readcount values for each sample

organism: Taeniopygia guttata

source_name: TN

extract_protocol:
Total RNA was isolated from the aqueous layer produced after chloroform precipitation, using the RNA Clean & Concentrator Kit-5 (Zymo Research, item # R1013) following manufacturer’s instructions and including the DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols

value: TN

tag: social treatment

value: KFC

tag: injection treatment

value: L


title: SG4_ChIP_BiorepA_rep2


title: KFC S TN70

value: S


title: SG4_ChIP_U2OS_inupt_BioRepC

value: input library


title: SG4_ChIP_BiorepA_rep3


title: KFC L TN69


title: SG4_ChIP_U2OS_inupt_BioRepB


title: SG4_ChIP_BiorepA_rep1


title: KFC S TN68


title: KFC L TN67


title: KFC S TN66


title: SG4_ChIP_U2OS_inupt_BioRepA


title: KFC L TN65


title: SG4_ChIP_U2OS_BioRepC_Rep2


title: KFC S TN63


title: SG4_ChIP_BiorepB_rep3


title: SG4_ChIP_U2OS_BioRepC_Rep1


title: KFC L TN64


title: KFC S TN62


title: SG4_ChIP_U2OS_BioRepB_Rep2


title: SG4_ChIP_U2OS_BioRepB_Rep1


title: NF L TN59

value: NF


title: SG4_ChIP_U2OS_BioRepA_Rep3


title: ISO L TN56

value: ISO


title: ISO S TN53


title: NF S TN58


title: SG4_ChIP_U2OS_BioRepA_Rep2


title: Size matched input for 14-3-3 motif mutant SAMD4A-EGFP

city: Toronto

first: Mikko

last: Taipale

state: Ontario

address: 160 college street

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: Extracted RNA was reverse transcribed using primer Rt7clip/5Phos/NNCTAANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNCTAANNN, where N are random bases.

data_processing:
iCLIP libraries with XXXNNNNXX barcodes, where X is a random nucleotide, were demultiplexed and trimmed using cutadapt (ver 2.10). The PCR duplicates were collapsed using UMI-tools. Then, the processed iCLIP reads were mapped to Gencode assembly GRCh37.p13 (hg19)  using STAR aligner (v2.7.1). To identify the SAMD4A mRNA targets, peak calling was performed on the uniquely mapped reads using Pureclip with default settings, replicates and input as a covariate. The resulting binding regions were annotated by overlapping GRCh37 gene annotations using bedtools (ver 2.29.2).
Assembly: hg19
Supplementary files format and content: Comma-separated values file containing chromosome, start, end, and strand of bound region, as well as Ensemble gene ID and gene symbol (name) of bound genes. Also includes PureCLIP scores for the binding region.

source_name: cervical carcinoma

growth_protocol: HeLa cell lines with stable integrations of wild-type or 14-3-3 motif mutant SAMD4A tagged at the C-terminus with EGFP were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were maintained in a humidified incubator at 37°C and 5% CO2.

extract_protocol: Cells were UV cross-linked with 0.15 J/cm2 at 254 nm in a Stratalinker 1800 after induction with doxycycline (1 μg/ml) for 24 hours. Cells were lysed in 2.2 ml of iCLIP lysis buffer (50 mM Tris–HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with protease inhibitors. To digest the genomic DNA and obtain RNA fragments of an optimal size range, 1 ml of lysate was incubated with Turbo DNase (Thermo Fisher Scientific, AM2238) and RNase I (1:250; Thermo Fisher Scientific, AM2294) for exactly 5 minutes at 37°C. EGFP-tagged proteins were immunoprecipitated using 5 μg of anti-GFP antibody (Abcam, ab290). A total of 2% input material was set aside for size-matched control libraries (SMI) prior to immunoprecipitation. Following three stringent washes with iCLIP high salt buffer (50 mM Tris–HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and dephosphorylation with FastAP and T4 polynucleotide kinase, onbead-ligation of pre-adenylated adaptors to the 3’ ends of RNAs was performed using the enhanced CLIP ligation method. The immunoprecipitated RNA was 5’-end-labeled with 32P using T4 polynucleotide kinase (New England Biolabs, M0201L). The protein-RNA complexes from the IP and SMI were separated using 4–12% BisTris–PAGE and transferred to a nitrocellulose membrane (Protran). For the SMI, the membrane was cut to match the size of the IP material. RNA was recovered by digesting proteins using proteinase K (Thermo Fisher, 25530049) and subsequently reverse transcribed into cDNA using barcoded primers. The cDNA was size-selected (low: 70 to 85 nt, middle: 85 to 110 nt, and high: 110 to 180 nt) using 6% TBE-urea and circularized using CircLigase™ II ssDNA ligase to add the adaptor to the 5’ end. To enhance the circularization, betaine in the CircLigase reaction was added at a final concentration of 1 M, and the reaction mixture was incubated for at least 2 hours at 60°C. Circularized cDNA was digested at the internal BamHI site for linearization, and PCR amplified using Phusion High-Fidelity PCR Master Mix (NEB, M0531S). The final PCR libraries were agarose gel purified on purification columns (Qiagen), and the eluted DNA was mixed at a ratio of 1:5:5 from the low, middle, and high fractions and submitted for sequencing on Illumina NextSeq 500 platform using a full High-Output v2.5 flow cell to generate single-end 51 nucleotide reads with 40M read depth per sample.

treatment_protocol: Crosslinking (0.15 J/cm2) was done at 254 nm with a Stratalinker 1800.

value: HeLa cells overexpressing 14-3-3 motif mutant SAMD4A-EGFP

value: Expression of stably integrated 14-3-3 motif mutant SAMD4A-EGFP was induced with 1 μg/mL of doxycycline for 24 hours prior to UV crosslinking.


title: SG4_ChIP_U2OS_BioRepC_Rep3


title: ISO S TN52


title: SG4_ChIP_U2OS_BioRepA_Rep1


title: KF L TN48

value: KF


title: KF S TN47


title: ISO S TN50


title: KF S TN44


title: iCLIP-seq of wild-type SAMD4A-EGFP, replicate 2

description: Extracted RNA was reverse transcribed using primer Rt13clip/5Phos/NNTCCGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTCCGNNN, where N are random bases.

value: HeLa cells overexpressing wild-type SAMD4A-EGFP

value: Expression of stably integrated wild-type SAMD4A-EGFP was induced with 1 μg/mL of doxycycline for 24 hours prior to UV crosslinking.

tag: antibody

value: GFP polyclonal antibody (Abcam, ab290)


title: iCLIP-seq of wild-type SAMD4A-EGFP, replicate 1

description: Extracted RNA was reverse transcribed using primer Rt12clip/5Phos/NNGTGGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGTGGNNN, where N are random bases.


title: Size matched input for wild-type SAMD4A-EGFP

description: Extracted RNA was reverse transcribed using primer Rt15clip/5Phos/NNTATTNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTATTNNN, where N are random bases.


title: iCLIP-seq of 14-3-3 motif mutant SAMD4A-EGFP, replicate 2

description: Extracted RNA was reverse transcribed using primer Rt14clip/5Phos/NNTGCCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNTGCCNNN, where N are random bases.


title: iCLIP-seq of 14-3-3 motif mutant SAMD4A-EGFP, replicate 1

description: Extracted RNA was reverse transcribed using primer Rt9clip/5Phos/NNGCCANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNGCCANNN, where N are random bases.


title: KF S TN42


title: SG4_ChIP_U2OS_BioRepB_Rep3


title: KF L TN41


title: RNA-seq of doxycycline induced 14-3-3 motif mutant SAMD4A-EGFP HeLa cells, replicate 1

description: SAMD4A MUT +DOX 1

data_processing:
Reads were aligned to the Gencode human primary assembly (GRCh38.p13) with STAR aligner v2.7.3a
The Gencode transcript annotations were then used to generate counts for each gene
Stranded raw read counts for all genes in the SAMD4A-EGFP overexpression experiments were compiled into a single file
Gene expression changes comparing induced cells to uninduced cells from the same cell line were quantified using the edgeR package on the public server at usegalaxy.org
lowly expressed genes were filtered out and counts were normalized for varying sequencing depths using a trimmed mean of M values (TMM) method
P-values for the Log2 fold changes of each gene were adjusted using the Benjamini and Hochberg method
Assembly: hg38
Supplementary files format and content: Tab-separated values for differential expression analysis and Comma separated values for raw read counts

extract_protocol:
RNA was extracted from cells using the RNeasy purification kit (Qiagen) and treated with DNase on a column
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-seq with Poly-A enrichment kit

treatment_protocol: Expression of stably integrated wild-type or 14-3-3 motif mutant SAMD4A-EGFP was induced with 1 μg/mL of doxycycline for 48 hours prior to RNA extraction.

value: Expression of stably integrated 14-3-3 motif mutant SAMD4A-EGFP was induced with 1 μg/mL of doxycycline for 48 hours prior to RNA extraction.


title: RNA-seq of doxycycline induced 14-3-3 motif mutant SAMD4A-EGFP HeLa cells, replicate 2

description: SAMD4A MUT +DOX 2


title: Prepubertal_BOV_testis2_H12

city: Pullman

first: Jon

last: Oatley

state: WA

address: 202 Biotechnology Life Science Building  PO Box 647520,

department: School of Molecular Biosciences

institute: Washington State University

description: 10x Genomics

data_processing:
Raw base call files were demultiplexed using the 10X Genomics Cell Ranger pipeline (v2.1.0)
Assembly: Bovine genome (ARS-UCD1.2) or porcine genome (Sscrofa11.1).
Supplementary files format and content: Barcodes (.tsv and .gz), Features(.tsv and .gz) and matrix (.mtx)

organism: Bos taurus

source_name: Testis

extract_protocol:
Testes from pre-pubertal Holstein breed cattle and mixed breed pigs were collected by castration. For all samples, single-cell suspensions of testicular parenchyma were generated as described previously (Oatley and Brinster, 2006; Oatley et al., 2016).
Live cells (~8000 per sample) were then loaded into a Chromium Controller (10X Genomics, Inc.), and cDNA libraries were generated using v2 chemistry kits (10X Genomics, Inc.). Libraries were pooled at proportions netting equal read depth and sequenced in a single lane on an Illumina HiSeq 4000 (Genomics and Cell Characterization Core Facility, University of Oregon).

value: Total testicular cells

value: Testis

tag: strain

value: Holstein

tag: age

value: 4.5 months old


title: Prepubertal_SUS_testis2_P4

description: 10x Genomics

organism: Sus scrofa

tag: cell type

value: mixed breed

value: 3 months old


title: NF S TN39

value: TN

value: S


title: Prepubertal_SUS_testis2_P5

description: 10x Genomics


title: Prepubertal_SUS_testis1_B5

description: 10x Genomics


title: Prepubertal_BOV_testis2_H11

description: 10x Genomics


title: RNA-seq of uninduced 14-3-3 motif mutant SAMD4A-EGFP HeLa cells, replicate 2

description: SAMD4A MUT 2

value: HeLa cells (contains stably integrated 14-3-3 motif mutant SAMD4A-EGFP)


title: NF S TN37

value: NF


title: Prepubertal_BOV_testis1_B6

description: 10x Genomics


title: total-RNA_Siwi-KD_rep2

data_processing:
total RNA sequencing: After cleaning raw reads and removal of adaptor sequences using Rcorrector (version 1.0.4) (Song et al. 2015), TranscriptomeAssemblyTools (https://github.com/harvardinformatics/TranscriptomeAssemblyTools), and TrimGalore (version 0.6.6) (https://github.com/FelixKrueger/TrimGalore), reads shorter than 36 nt were discarded. The reads were mapped against the genome and remapped against the silkworm gene library using STAR in random and multiple counting modes allowing up to 4% mismatches relative to read length. Gene-mapped reads from the total RNA sequencing data were processed using SAMtools. The reads mapped to the sense direction were normalized against the number of genome-mapped reads to RPKM with the addition of a pseudo-count for log transformation and FC calculation. Owing to the high correlation of replicate samples, the two replicate reads were merged for further analysis.
Assembly: the Bombyx mori genome assembly (Nov 2016) (Kawamoto et al. 2019) from the SilkBase database
Supplementary files format and content: total RNA sequencing: Tab-separated text files include normalized count of reads (RPKM) mapped to the silkworm gene library in sense direction.

source_name: Cultured cell derived from ovary

extract_protocol:
total RNA sequencing: BmN4 cells treated with Luc (control) or Siwi siRNA were used for RNA sequencing. Total RNAs were isolated using ISOGEN II (FUJIFILM Wako Pure Chemical) and DNase (Life Technologies).
total RNA sequencing: RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) with the Ribo-Zero Plus rRNA Depletion Kit (Human/Mouse/Rat) (Illumina) and sequenced on the NovaSeq platform (Illumina) to obtain paired-end reads, resulting in 77,614,516 and 68,702,400 reads for Luc KD and 81,135,072 and 77,184,922 reads for Siwi KD (Replicates 1 and 2, respectively).

value: Cultured cell derived from ovary

value: Siwi KD

value: RNAi


title: total-RNA_Luc-KD_rep2

value: Control (Luc KD)


title: KF S TN36

value: KF


title: KF L TN35

value: L


title: RNA-seq of doxycycline induced wild-type SAMD4A-EGFP HeLa cells, replicate 2

description: SAMD4A WT +DOX 2

value: HeLa cells overexpressing wild-type SAMD4A-EGFP

value: Expression of stably integrated wild-type SAMD4A-EGFP was induced with 1 μg/mL of doxycycline for 48 hours prior to RNA extraction.


title: RNA-seq of uninduced wild-type SAMD4A-EGFP HeLa cells, replicate 2

description: SAMD4A WT 2

value: HeLa cells (contains stably integrated wild-type SAMD4A-EGFP)


title: KF S TN34


title: RNA-seq of uninduced wild-type SAMD4A-EGFP HeLa cells, replicate 1

description: SAMD4A WT 1


title: total-RNA_Siwi-KD_rep1


title: KF L TN33


title: RNA-seq of doxycycline induced wild-type SAMD4A-EGFP HeLa cells, replicate 1

description: SAMD4A WT +DOX 1


title: KF L TN30


title: KF L TN32


title: mutDBD_IRF4_IP [PAD_186]

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

institute: Institut Imagine

data_processing:
Mapping with bwa
Removal of duplicate reads
In silico extension of the 5 ́-ends of the aligned reads (tags) at their 3 ́- ends to a length of 200 bp (using Active Motif software)
Peak calling with MACS2
Assembly: GRCh38/hg38
Supplementary files format and content: BigWig files for each sample

source_name: EBV-B

growth_protocol: Peripheral blood samples were collected from the patients after the provision of written, informed consent. Genetic studies and data collection procedures were approved by the local independent ethic committee (Comité de Protection des Personnes Ile de France II, Paris, France; reference: 2015-01-05; 2015-01-05 MS2) and the French Advisory Committee on Data Processing in Medical Research (reference: 15.297bis). EBV-B cells were cultured in RPMI medium supplemented with 10% FBS

extract_protocol:
B-EBV cells (10x106) from P3 and a healthy control C1 were fixed with freshly prepared 1% formaldehyde (#F-8775, Sigma) for 15 min and quenched with 0.125M glycine (Sigma #G-7403) for 5 min, washed twice with 1x PBS containing 0.5% Igepal CA-630 (Sigma #I-8896), the second time in the presence of 1M Phenylmethanesulfonyl fluoride. Cell pellets were snap frozen and subjected to ChIP-seq.
Chromatin extraction, IP using IRF4 antibody (Cell Signalling, #4948), library preparation, next generation sequencing and a Model-based Analysis of ChIP-Seq (41) was performed by Active Motif (Carlsbad, CA)

tag: status

value: EBV-B

tag: ip antibody

value: IRF4 antibody


title: mutIAD_IRF4_IP [PAD_156_2]


title: Healthy_control_IRF4_IP [PAD_114]

value: Control


title: NF S TN20


title: NF L TN24


title: KF S TN31


title: NF L TN19


title: Day 15, CD200 High

data_processing:
Reads were mapped to mouse genome GRCm38 using STAR Aligner and gene-based readcounts were generated using HTSeq
Differential gene expression was performed in edgeR after library size normalization. CPM values were compared.
Assembly: GRCm38
Supplementary files format and content: .xlsx spreadsheet containing CPM values

growth_protocol: Growth plate like chondrocyte (GPLC) cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 100 U/mL Penicillin/ 100mg/mL Streptomycin,  50 ug/mL Ascorbic acid, and 1X Insulin/Transferrin/Selenium in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from sorted cells using QIAGEN Rneasy Plus Mini Kit and concentrations were quantified using NanoDrop.
Libraries were prepared by the Harvard Medical School's Biopolymers Facility via KAPA HyperPrep with Ribo-Erase Library Prep

tag: time

value: Day 15

tag: sorted group

value: CD200 High


title: Day 15, CD200 Low

source_name: Growth plate like chondrocyte (GPLC) cells

value: CD200 Low


title: AgedPBMale3 Biol rep 3

city: Ithaca

first: Abigail

last: Benvie

address: 526 Campus Rd

institute: Cornell University

description:
AGEDPB3 in processed data
AGED_AGEDPB2_norm.count.csv

data_processing:
Basic analysis including preprocessing, mapping to reference genome, and gene expression analysis to generate normalized counts and statistical analysis of differential gene expression
reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt  and fastQC .
reads were mapped to the reference genome/transcriptome using STAR v2.7.0e
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression
Assembly: reference genome: Ensembl GRCm38
Supplementary files format and content: CSV files including all samples used in analysis, indivudal normalized counts, and gene names/IDs  across groups

source_name: Adipose

extract_protocol:
RNA was extracted using the standard chloroform extraction and isopropanol precipitation method. RNA concentrations and quality were determined using a TECAN infinite F-nano+ spectrophotometer.
750 ng of Poly (A) enriched RNA was used for directional RNAseq library preparation using the NEBNext Ultra II RNA Library Prep Kit according to standard protocol.

value: Adipose

value: primary cells from adipose tissue

value: PdgfrB Knock Out

value: 12 month old


title: AgedPbMale2 Biol rep 2

description:
AGEDPB2 in processed data
AGED_AGEDPB2_norm.count.csv


title: total-RNA_Luc-KD_rep1

value: Cultured cell derived from ovary

value: RNAi


title: AgedPBMale1 Biol rep 1

description:
AGEDPB1 in processed data
AGED_AGEDPB2_norm.count.csv


title: ISO L TN16

value: TN

value: ISO


title: RNA-seq of uninduced 14-3-3 motif mutant SAMD4A-EGFP HeLa cells, replicate 1

description: SAMD4A MUT 1

value: HeLa cells (contains stably integrated 14-3-3 motif mutant SAMD4A-EGFP)


title: AgedMale4 Biol rep 4

description:
12MO4 OR AGED4 in processed data
YOUNG_OLD3_norm.count.csv and AGED_AGEDPB2_norm.count.csv

value: wild type


title: Day 4, CD200 High

value: Growth plate like chondrocyte (GPLC) cells

value: Day 4


title: AgedMale2 Biol rep 2

description:
12MO2 OR AGED2 in processed data
YOUNG_OLD3_norm.count.csv and AGED_AGEDPB2_norm.count.csv


title: AgedMale1 Biol rep 1

description:
12MO1 or AGED1 in processed data
YOUNG_OLD3_norm.count.csv and AGED_AGEDPB2_norm.count.csv


title: ISO S TN13

value: S


title: Day 4, CD200 Low


title: NF L TN27

value: NF

value: L


title: YoungMale4 Biol rep 4

description:
2MO4 in processed data
YOUNG_OLD3_norm.count.csv

value: 2 month old


title: A7

city: Monrovia

first: Srividya

last: Swaminathan

address: 1218 fifth Ave

department: Systems biology

institute: Beckman Research Institute, City of Hope

data_processing:
Experiment Workflow (Provide cDNA, amplify )
Sequenced (MiSeq Illumina 2x150 bp platform)
Supplementary files format and content: xls files include reads for Unique sequences of nucleotides in each sample
Supplementary files format and content: xls files include reads for Unique sequences of aminoacids in each sample
Library strategy: IGH repertoire

source_name: Spleen

extract_protocol:
Using Machery Nagel kits to isolate RNA and using PCR primers for VHJ558 variable and Cμ constant regions for IGH amplification
TrueSeq library was prepared by adapter ligation to full-length products and sequenced on the MiSeq Illumina 2x150 bp platform

value: spleen

value: B cells

value: MRL/lpr SLE prone

value: 14 weeks

tag: Sex

value: F

value: LFPRLR SMO


title: ISO L TN14


title: YoungMale3 Biol rep 3

description:
2MO3 in processed data
YOUNG_OLD3_norm.count.csv

value: Adipose

value: primary cells from adipose tissue


title: Input [0A5K_Pooled_Input]

value: Input (pooled)

value: EBV-B

value: none (input)


title: A6


title: AgedPBMale4 Biol rep 4

description:
AGEDPB4 in processed data
AGED_AGEDPB2_norm.count.csv

value: PdgfrB Knock Out

value: 12 month old


title: YoungMale1 Biol rep 1

description:
2MO1 in processed data
YOUNG_OLD3_norm.count.csv

value: wild type


title: ISO S TN12

value: TN

value: ISO

value: S


title: ISO L TN9

value: L


title: Anti-TNFα mAb group 3

city: hiroshima

first: Takeshi

last: Takasago

state: hiroshima

address: kasumi 1-2-3

department: Gastroenterology

institute: Hiroshima university hospital

data_processing:
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38)
The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0)
The HISAT2-resultant .sam files were converted into .bam files with samtools  and used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3)
The raw counts were normalized with transcripts per million (TPM)
Supplementary files format and content: xlsx files include Raw count Matrix and TPM matrix for each Sample

source_name: Colon adenocarcinoma (orthotopic transplantation)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 20 μl of total RNA was used for the construction of sequencing libraries.
Poly(A) RNA preparation: Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA),Library preparation: NEBNext® Ultra™II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA)

treatment_protocol: The CT26 mouse colon cancer cell line were transplanted into the cecum of BALB/c mice. Mice were divided into two groups: one group received not reatment, and the other group received anti-TNFα mAb (MP6-XT22) treatment every 7 days after transplantation. On day 21after transplantation, cecal tumors from each group were excised for  gene expression profiling analysis .

value: Colon adenocarcinoma

value: anti-TNFα mAb


title: YoungMale2 Biol rep 2

description:
2MO2 in processed data
YOUNG_OLD3_norm.count.csv

value: 2 month old


title: A5

value: spleen

value: B cells

value: MRL/lpr SLE prone

value: 14 weeks

value: F


title: ISO L TN8


title: Anti-TNFα mAb group 1

value: Colon adenocarcinoma (orthotopic transplantation)


title: A4

value: LFPRLR SMO


title: ISO L TN6


title: Control group 2

value: Control


title: A3


title: AgedMale3 Biol rep 3

description:
12MO3 OR AGED3 in processed data
YOUNG_OLD3_norm.count.csv and AGED_AGEDPB2_norm.count.csv

value: Adipose

value: primary cells from adipose tissue

value: 12 month old


title: A8


title: Control group 1


title: Control group 3


title: C9

value: Control SMO


title: NF S TN4

value: TN

value: NF

value: S


title: Sample 10, female biol rep 6, snRNAseq

city: Bethesda

first: Claire

last: Gao

state: MD

address: 35 Covent Dr, Bldg 35 Rm 2E-614G

department: Unit on the Neurobiology of Affective Memory

institute: NIMH

description:
10x Genomics
allnuclei_barcodes.tsv
allnuclei_genes.tsv
allnuclei_matrix.mtx

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10.3.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: paraventricular thalamus

extract_protocol:
Mechanical -Detergent Lysis Protocol described by Matson et. al. 2018 (JoVe) was used to create nuclei suspensions. Fresh PVT tissue punches were collected and mechanically lysed in lysis buffer using a Dounce homogenizer tube. Crude nuclei preparation were filtered and washed using low sucrose buffer. Nuclei prep were then centrifuged and reconstituted using low sucrose buffer. Following mechanical homogenization, nuclei prep were pased through a sucrose density gradient to cleanse the sample of debris. Following centrifugation, the nuclei were resuspended in a 0.04%BSA solution for sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: brain cells

value: paraventricular thalamus

value: 12 weeks old


title: Sample 8, female biol rep 4, snRNAseq


title: KFC L NST71

source_name: NS

value: NS

value: KFC

value: L


title: Sample 7, female biol rep 3, snRNAseq


title: KFC S NST70


title: C7

value: spleen

value: B cells

value: MRL/lpr SLE prone

value: 14 weeks

value: F


title: Sample 6, female biol rep 2, snRNAseq


title: Anti-TNFα mAb group 2

value: Colon adenocarcinoma (orthotopic transplantation)

value: Colon adenocarcinoma

value: anti-TNFα mAb


title: Sample 5, female biol rep 1, snRNAseq


title: KFC L NST69


title: C3

value: Control SMO


title: KFC S NST68


title: C5


title: KFC S NST66


title: KFC L NST67


title: Tumor implanted; tumor regressed; 1008226_TCR

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description: 10x Genomics

data_processing:
Cell Ranger Single-Cell Software Suite (10X Genomics, v2.2.0) was used to perform sample demultiplexing, alignment, filtering, and UMI counting.
Assembly: GRCh38
Supplementary files format and content: scRNA-Seq tab-delimited text file include read count for each sample
Supplementary files format and content: scTCR-Seq filtered_contig_annotations file
Library strategy: scTCR-Seq

extract_protocol:
Single cells suspended in PBS with 0.04% BSA (~6000 cells) were loaded on a Chromium Single Cell Instrument (10X Genomics).
RNA-seq and V(D)J libraries were prepared using Chromium Single Cell v1.0 5’ Library, Gel Beads & Multiplex Kit (10X Genomics)

value: hCD45+/hCD3+ T cells

value: tumor

value: Tumor implanted; tumor regressed


title: Type 2 Control Sample 4

city: New York

first: Mollie

last: Chipman

department: Cancer Biology and Genetics

institute: Sloan Kettering Institute

data_processing:
Libraries were aligned to the mouse genome (GRCm38-100 ) and gene expression counted using STAR (Version 2.7.8a). Downstream bioinformatics analysis was performed in R  using the DESeq2 package (Love et al., 2014) for normalization and differential gene expression analysis.
Type 1 and Type 2 tumors were either analyzed together or separately. The Total NormCounts file has all tumors analyzed together TAM depleted vs. Control.
The Type1NormCounts and Type2NormCounts files has the Type 1 samples, and Type 2 samples, analyzed separately, TAM depleted vs. control
Assembly: mm11
Supplementary files format and content: Tab-delimited files contain DESeq2 normalized counts

source_name: Tumor

extract_protocol:
Phase separation in cells lysed in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro Kit (Qiagen catalog # 217084) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit  following manufacturer's protocols.

value: Tumor

tag: tumor type

value: Type 2 Control

tag: model

value: Transplanted


title: Type 2 Control Sample 2

tag: tissue


title: Type 2 TAM depleted Sample 4

value: Type 2 TAM depleted


title: Sample 9, female biol rep 5, snRNAseq

value: brain cells

value: paraventricular thalamus

value: 12 weeks old


title: Type 1 Control Sample 5

value: Type 1 Control


title: KFC L NST65

value: NS

value: KFC

value: L


title: Type 2 TAM depleted Sample 1


title: Type 2 TAM depleted Sample 2


title: Tumor implanted; tumor regressed; 1008224_TCR

description: 10x Genomics

source_name: spleen

value: spleen


title: C8

value: B cells

tag: genotype

value: MRL/lpr SLE prone

value: 14 weeks

value: F


title: Tumor implanted; tumor outgrowth; 1008223_TCR

description: 10x Genomics

value: hCD45+/hCD3+ T cells

value: Tumor implanted; tumor outgrowth


title: Type 1 Control Sample 4

value: Tumor


title: ISO S TN5

value: TN

value: ISO

value: S


title: Type 1 TAM depleted Sample 3

value: Type 1 TAM depleted

value: Transplanted


title: Type 2 TAM depleted Sample 3

value: Type 2 TAM depleted


title: Type 2 Control Sample 3

value: Type 2 Control


title: Type 2 Control Sample 1


title: C4

value: Control SMO


title: KFC L NST64

value: NS

value: KFC

value: L


title: Type 1 TAM depleted Sample 2


title: Tumor implanted; tumor regressed; 1006830_TCR

description: 10x Genomics

value: tumor

value: Tumor implanted; tumor regressed


title: Type 1 Control Sample 2

value: Type 1 Control


title: Type 1 Control Sample 3


title: Type 1 TAM depleted Sample 1


title: KFC S NST63


title: Tumor implanted; tumor regressed; 1006828_TCR

description: 10x Genomics

value: hCD45+/hCD3+ T cells

value: spleen


title: Type 1 Control Sample 1

value: Tumor


title: WT brain sorted Microglia, Sample 4

data_processing:
Libraries were aligned to the mouse genome (mm10) and gene expression counted using STAR (Version 2.7.8a). Downstream bioinformatics analysis was performed in R  using the DESeq2 package (Love et al., 2014) for normalization and differential gene expression analysis.
N/A
N/A
N/A
N/A
Assembly: mm11
Supplementary files format and content: Tab-delimited files contain DESeq2 normalized counts
Supplementary files format and content: N/A

source_name: Brain

value: Brain

tag: cell line

value: Microglia

value: Non-tumor


title: Tumor implanted; tumor regressed; 1006827_TCR

description: 10x Genomics


title: Type 2 transplanted tumor sorted Microglia, Sample 3


title: Tumor implanted; no tumor growth; 1005916_TCR

description: 10x Genomics

value: Tumor implanted; no tumor growth


title: Tumor implanted; no tumor growth; 1005917_TCR

description: 10x Genomics


title: NF S NST58

value: NF

value: S


title: KFC S NST62


title: Type 2 transplanted tumor sorted MDM, Sample 2

value: MDM

value: Transplanted


title: NF L NST59

value: NS


title: Type 2 transplanted tumor sorted Microglia, Sample 1


title: WT brain sorted Microglia, Sample 3


title: ISO L NST56

value: ISO


title: WT brain sorted Microglia, Sample 1


title: No tumor ; 1005915_TCR

description: 10x Genomics

value: No tumor


title: Type 2 transplanted tumor sorted MDM, Sample 1


title: Type 2 spontaneous tumor sorted Microglia, Sample 3

value: Spontaneous


title: No tumor ; 1005914_TCR

description: 10x Genomics


title: NF L NST57

value: L


title: Type 2 transplanted tumor sorted Microglia, Sample 2


title: ISO S NST53


title: Type 2 spontaneous tumor sorted MDM, Sample 1


title: Tumor implanted; tumor outgrowth; 984888_TCR

description: 10x Genomics

source_name: tumor

value: tumor

value: Tumor implanted; tumor outgrowth


title: Type 2 spontaneous tumor sorted Microglia, Sample 1


title: Tumor implanted; tumor outgrowth; 984887_TCR

description: 10x Genomics

value: hCD45+/hCD3+ T cells


title: Type 2 spontaneous tumor sorted Microglia, Sample 2

value: Tumor


title: ISO S NST50


title: ISO S NST52


title: Tumor implanted; tumor outgrowth; 984886_TCR

description: 10x Genomics


title: Type 1 transplanted tumor sorted MDM, Sample 4


title: WT brain sorted Microglia, Sample 2

value: Brain


title: Type 1 transplanted tumor sorted MDM, Sample 3


title: Type 1 transplanted tumor sorted Microglia, Sample 2

value: Microglia


title: Type 1 transplanted tumor sorted MDM, Sample 2


title: Type 1 transplanted tumor sorted Microglia, Sample 1


title: Tumor implanted; tumor outgrowth; 984885_TCR

description: 10x Genomics

value: spleen


title: Type 1 transplanted tumor sorted MDM, Sample 1


title: Tumor implanted; tumor outgrowth; 984884_TCR

description: 10x Genomics


title: KF S NST47

value: KF


title: KF S NST44


title: Type 1 spontaneous tumor sorted Microglia, Sample 3


title: KF S NST42


title: Tumor implanted; tumor outgrowth; 984883_TCR

description: 10x Genomics


title: Tumor implanted; tumor outgrowth; 984351_TCR

description: 10x Genomics


title: Type 1 spontaneous tumor sorted Microglia, Sample 1


title: Type 1 transplanted tumor sorted Microglia, Sample 3


title: KF L NST41


title: Type 1 spontaneous tumor sorted MDM, Sample 1


title: Type 1 spontaneous tumor sorted MDM, Sample 2


title: Tumor implanted; tumor regressed; 984350_TCR

description: 10x Genomics

value: Tumor implanted; tumor regressed


title: NF S NST37

value: NF

value: S


title: LIP928-2XBP1s (ChIP-seq)

city: Wuhan

first: Faming

last: Zhao

state: Hubei

address: Hangkong road 13

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Quality control using fastQC version 0.11.9
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.4.3 with the default parameters.
Duplicate reads removal using sambamba version 0.8.1
MACS software was applied for peak calling, and Homer was used for motif analyses.
tab-delimited text file containing raw read counts for all samples
Assembly: hg38
Supplementary files format and content: BW files were generated using bamCoverage version 3.5.1.

growth_protocol: HepG2 cells were cultured in regular growth medium (DMEM + 10% FBS + 1%P/S)

extract_protocol:
Chromatin was sheared using the Bioruptor sonicator (VXC-750, Sonics, USA). After centrifugation, sheared chromatin was immunoprecipitated overnight with XBP1s antibody (#647502, BioLegend, USA), or mouse IgG.
The NEXTFLEX® ChIP-Seq Library Prep Kit was used for library generation according to Illumina's protocol.

treatment_protocol: Cells were treated with 30 nM Thapsigargin (Tg) for 3 hours.

value: human HCC cell line

tag: treatment

value: Thapsigargin

tag: chip antibody

value: anti-XBP1s (BioLegend, #647502)


title: IP928-1XBP1s (ChIP-seq)


title: Tumor implanted; tumor outgrowth; 984349_TCR

description: 10x Genomics


title: KF S NST36

value: NS

tag: social treatment

tag: injection treatment


title: L444P/L444P_DIV40 I3

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

institute: Institut Imagine, INSERM UMR1163

data_processing:
The sequencing data was analyzed with the Cell Ranger software (version 6.0.1) provided by 10x Genomics. Demultiplexing of the sequencing reads was performed with cellranger mkfastq.
For each sample, FASTQ files generated with cellranger mkfastq were subsequently processed with cellranger count. Cellranger count performs alignment, filtering, barcode counting and UMI counting. Using the filtered barcodes, it also generates feature-barcode matrices
Assembly: GRCh38-3.0.0
Supplementary files format and content: cellranger output files for raw gene-barcode matrix (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz)

source_name: Midbrain organoid

growth_protocol: Midbrain organoids were generated and maintained using a protocol developed in our group combining a previous methos that promotes midbrain floor-plate formation (Jo et al., 2016)

extract_protocol:
RNA libraries were prepared using standard 10X Genomics 3' Single Cell v2 protocol.
Cells loaded to Chromium Chip (target cell recovery): 10,000 cells. Library Preparation Kit: Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics). Sequencing parameters: NovaSeq 6000, SP Flow Cell, 100 cycles. Read 1: 28 bp, i7-index: 10 bp, i5-index 10 bp, Read 2: 90 bp. Q30 value: 91,88%

treatment_protocol: Midbrain organoids were dissociated into single-cell suspension following the Worthington Papain Dissociation System kit instructions (Worthington Biochemical) with intermittent trituration steps. The final solution was centrifuge 300g per 7 min, cell pellet were resuspended in PBS-0,04% BSA and filtered twice (40um, 30um) to obtain single-cell suspensions.

tag: source

value: iPSC-derived midbrain organoids

value: Day 40 of differentiation

value: Individual organoid 3


title: Tumor implanted; tumor regressed; 984348_TCR

description: 10x Genomics


title: Sample 3, biol rep 3, snRNAseq

description:
10x Genomics
CG6039-2

value: brain cells

value: paraventricular thalamus

tag: strain

tag: age

value: 12 weeks old


title: No tumor ; 983842_TCR

description: 10x Genomics

tag: cell type

value: hCD45+/hCD3+ T cells

tag: status

value: No tumor


title: KF L NST35

value: L


title: Sample 1, biol rep 1, snRNAseq

description:
10x Genomics
CG5745-1


title: No tumor ; 983841_TCR

description: 10x Genomics

value: spleen


title: Sample 2, biol rep 2, snRNAseq

description:
10x Genomics
CG5745-2


title: L444P/L444P 1_DIV40 I2

value: Individual organoid 2


title: Type 1 spontaneous tumor sorted Microglia, Sample 2

value: Tumor

value: Microglia

value: Spontaneous


title: KF S NST34

value: KF

value: S


title: KF L NST48

value: NS


title: Tumor implanted; tumor regressed; 1008226_RNA

description: 10x Genomics

data_processing:
Cell Ranger Single-Cell Software Suite (10X Genomics, v2.2.0) was used to perform sample demultiplexing, alignment, filtering, and UMI counting.
Assembly: GRCh38
Supplementary files format and content: scRNA-Seq tab-delimited text file include read count for each sample
Supplementary files format and content: scTCR-Seq filtered_contig_annotations file

value: tumor

value: Tumor implanted; tumor regressed


title: L444P/L444P 1_DIV40 I1

value: iPSC-derived midbrain organoids

value: Day 40 of differentiation

value: Individual organoid 1


title: KF L NST33

data_processing:
Data filtering: reads containing adapters, reads containing N > 10% and low quality reads were filtered out
Mapping was done using HISAT2
HTSeq (v0.6.1) was used to count numbers of mapped reads.
Assembly: taeGut3.2.4, release 96, downloaded from Ensembl
Supplementary files format and content: tab-delimited text file includes raw (not normalized) readcount values for each sample


title: NF S NST39

value: NF


title: Sample 4, biol rep 4, snRNAseq

description:
10x Genomics
CG6978-3

value: brain cells

value: paraventricular thalamus

value: 12 weeks old


title: M2R.3

first: Molly

last: Estill

address: 1 Gustave L. Levy Place

institute: Mount Sinai School of Medicine

data_processing:
Quality control was performed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/), adapter contaminants were trimmed using Trimmomatic (github.com/usadellab/Trimmomatic), reads were aligned to a custom-built reference genome (RXRα and GFP plasmid sequences were added to GENCODE GRCm38 genome) using hisat2 (daehwankimlab.github.io/hisat2/), duplicate reads were removed using Picard MarkDuplicate tool (broadinstitute.github.io/picard/), and finally count matrices were generated using the featureCounts function of the subread package (subread.sourceforge.net/featureCounts.html) and a comprehensive gene annotation file obtained from GENCODE (GRCm38 vM23). Reads mapping to the plasmid codon-optimized Rxra overexpression sequence were added to reads mapping to the endogenous Rxra sequence (ENSMUSG00000015846).
Assembly: GRCm38
Supplementary files format and content: RXRa_OE_countmatrix.txt is a text file containing the read counts for the bulk tissue RNA-seq. RXRa_D1D2_OE_countmatrix.txt is text file containing the read counts for the isolated D1 and D2 RNA-seq samples. Plasmid_RXRa_GFP_sequence.fa is a fasta file containing the sequences for RXRa and GFP that were added to the reference genome prior to read alignment.

source_name: Nucleus Accumbens

extract_protocol:
For bulk tissue RNAseq, RNA extraction was performed using the RNeasy Micro Kit (Qiagen) following manufacturer instructions. For cell-type-specific RNAseq, RNA was extracted from frozen TRIzol LS (Ambion) homogenates using the Direct-zol RNA Microprep Kit (Zymo Research) following manufacturer instructions.
For bulk tissue RNAseq, Sequencing libraries were prepared by Genewiz/Azenta with polyA selection and sequenced with Genewiz/Azenta on an Illumina HiSeq 4000 machine using a 2 × 150 bp pair-end read configuration to a minimum depth of 20 million reads per sample. For cell-type-specific RNAseq, ribo-depleted sequencing libraries were prepared with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa Biotech) following manufacturer instructions and sequenced with Genewiz/Azenta on an Illumina NovaSeq S4 machine using a 2 × 150 bp pair-end read configuration to a minimum depth of 40 million reads per sample.

value: Nucleus Accumbens

tag: gender

value: Male

tag: viral vector

tag: rna extraction kit


title: HD172_L368P IRF4 mutation

data_processing:
Mapping with HISAT2
Deduplication with Picard MarkDuplicates (AS=true VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true)
Sort with samtools sort (-n)
Assign to features using featureCounts (-p -F GTF; GENCODE-annotated genes )
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited table of raw read counts for GENCODE genes and for each sample
Supplementary files format and content: Tab-delimited table with the layout for processing

source_name: PBMC

growth_protocol: CD4+ and CD8+ naive T cells were isolated from PBMCs of healthy donors. , cells were labelled with anti-CD4 (#345768, BD), anti-CD8 (#345773, BD), anti-CD45RA (#304138, Biolegend), and anti-CCR7 (#130-099-363, Miltenyi) antibodies, and naive (defined as CD45RA+ CCR7+ CD4+) T cells were isolated (>98% purity) with a FACS AriaII cell sorter (BD Biosciences). Purified naive CD4+ or CD8+ T cells were activated with DynabeadsTM T cell activation (anti-CD3/CD28; #11131D, Gibco) and cultivated in IL-2 (300UI/mL) containing media. 24hrs later cells were transduced using a transduction adjuvant (Lentiboost, Sirion Biotech and PGE2 Cayman, #14750) with lentiviral vectors (pWPI backbone) expressing IRF4 WT or mutants.

extract_protocol:
RNA was prepared from 500,000 cells with the RNeasy Plus Kits (Qiagen) including a DNAse treatment step, according to the manufacturer’s instructions. RNA quality was assessed by capillary electrophoresis using High Sensitivity RNA reagents with the Fragment Analyzer (Agilent Technologies) and the RNA concentration were measured by using both spectrophometry using the Xpose (Trinean) and Fragment Analyzer capillary electrophoresis.
Libraries were prepared starting from 200ng of total with the Universal Plus mRNA-Seq kit (Nugen) as recommended by the manufacturer (libraries can be prepared from 10 ng to 1µg of starting total RNA). The oriented cDNA produced from the poly-A+ fraction were sequenced on a NovaSeq6000 from Illumina (Paired-End reads 100 bases + 100 bases). A total of ~50 millions of passing filter paired-end reads was produced per library.


title: HD172_R98W IRF4 mutation


title: M2R.2

value: Direct-zol RNA Microprep Kit (Zymo Research)


title: KF L NST32

extract_protocol:
Total RNA was isolated from the aqueous layer produced after chloroform precipitation, using the RNA Clean & Concentrator Kit-5 (Zymo Research, item # R1013) following manufacturer’s instructions and including the DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols

value: L


title: Tumor implanted; tumor regressed; 1008224_RNA

description: 10x Genomics

value: hCD45+/hCD3+ T cells

value: spleen


title: Tumor implanted; tumor outgrowth; 1008223_RNA

description: 10x Genomics

value: Tumor implanted; tumor outgrowth


title: KF S NST31

value: NS

value: KF

value: S


title: M2R.1


title: Tumor implanted; tumor regressed; 1006830_RNA

description: 10x Genomics

value: tumor

value: Tumor implanted; tumor regressed


title: HD172_F359L IRF4 mutation


title: HD172_WT IRF4 sample

value: Control


title: KF L NST30


title: M2G.5


title: Tumor implanted; tumor regressed; 1006828_RNA

description: 10x Genomics


title: HD172_Empty vector


title: M2R.5


title: NF S NST28

value: NF


title: M2G.4


title: HD150_R98W IRF4 mutation


title: Tumor implanted; tumor regressed; 1006827_RNA

description: 10x Genomics


title: NF L NST27


title: M2G.3


title: Tumor implanted; no tumor growth; 1005917_RNA

description: 10x Genomics

value: Tumor implanted; no tumor growth


title: HD150_L368P IRF4 mutation


title: M2G.1


title: NF L NST24


title: Tumor implanted; no tumor growth; 1005916_RNA

description: 10x Genomics


title: NF S NST20


title: HD150_F359L IRF4 mutation


title: M2G.2


title: HD150_WT IRF4 sample


title: NF L NST19


title: M1R.5


title: HD150_Empty vector


title: No tumor ; 1005915_RNA

description: 10x Genomics

value: No tumor


title: Tumor implanted; tumor outgrowth; 984888_RNA

description: 10x Genomics


title: ISO L NST16

value: ISO


title: M1R.3

value: Nucleus Accumbens


title: HD98_R98W IRF4 mutation


title: No tumor ; 1005914_RNA

description: 10x Genomics


title: ISO L NST14


title: M1R.2

value: Male


title: M1R.1

value: Direct-zol RNA Microprep Kit (Zymo Research)


title: HD98_L368P IRF4 mutation


title: ISO S NST13


title: Tumor implanted; tumor outgrowth; 984887_RNA

description: 10x Genomics


title: Tumor implanted; tumor outgrowth; 984886_RNA

description: 10x Genomics


title: HD98_F359L IRF4 mutation


title: ISO S NST12


title: ISO L NST9

value: L


title: HD98_WT IRF4 sample


title: Tumor implanted; tumor outgrowth; 984884_RNA

description: 10x Genomics

value: hCD45+/hCD3+ T cells


title: ISO L NST8


title: HD98_Empty vector


title: ISO L NST6


title: Tumor implanted; tumor outgrowth; 984883_RNA

description: 10x Genomics

value: spleen


title: L444P/L444P 1 - GC_DIV100

value: iPSC-derived midbrain organoids

value: Day 100 of differentiation

value: L444P/L444P 1 - Gene corrected


title: Tumor implanted; tumor outgrowth; 984351_RNA

description: 10x Genomics

value: Tumor implanted; tumor outgrowth


title: L444P/L444P 1 - GC_DIV40

value: Day 40 of differentiation


title: Tumor implanted; tumor regressed; 984350_RNA

description: 10x Genomics

value: tumor

value: Tumor implanted; tumor regressed


title: mutDBD [PAD_186]

value: EBV-B


title: NF S NST4

value: NS

value: NF

value: S


title: ISO S NST5

value: ISO


title: Tumor implanted; tumor outgrowth; 984349_RNA

description: 10x Genomics


title: Tumor implanted; tumor regressed; 984348_RNA

description: 10x Genomics


title: NF L NST3


title: M1G.2

value: Nucleus Accumbens

value: Male


title: F2R.5

value: Female

value: Direct-zol RNA Microprep Kit (Zymo Research)


title: M1G.4


title: M1G.3


title: Tumor implanted; tumor outgrowth; 984885_RNA

description: 10x Genomics

value: hCD45+/hCD3+ T cells

value: spleen


title: KFC L HY71

source_name: HY

value: HY

value: KFC

value: L


title: M1G.1


title: M1G.5


title: No tumor ; 983842_RNA

description: 10x Genomics

value: No tumor


title: F2R.3


title: F2R.4


title: KFC S HY70


title: F2R.2


title: mutIAD [PAD_121]


title: No tumor ; 983841_RNA

description: 10x Genomics


title: KFC L HY69


title: L444P/L444P 1_DIV40

value: iPSC-derived midbrain organoids

value: Day 40 of differentiation

value: L444P/L444P 1 Mutant


title: F2R.1


title: Healthy_control [PAD_114]

value: Control

value: EBV-B


title: F2G.5


title: KFC S HY68

value: S


title: KFC L HY67


title: Atg7fl/fl LysMcre+/+ macrophages, mock infected, biol rep 2

city: Berkeley

first: Guillaume

last: Golovkine

address: 1951 Oxford Street

institute: UC Berkeley

data_processing:
remove adapter, polyA and low quality sequences using htstream/1.3.3, minimum read length after quality control is 50bp
map to GRCm39 using STAR (v2.7.9a)
deduplication using umi_tools (v1.1.2)
generate counts table using featureCounts function in subread package v1.6.3
Assembly: GRCm39
Supplementary files format and content: Excel file with mouse genes listed in the first column. Each sample in a separate column.

source_name: Bone-marrow derived macrophages

growth_protocol: Macrophages were seeded at a density of 2 x 106 cells per well in 6-well non-TC treated plate and incubated in DMEM, high glucose (Gibco) supplemented with 10% FBS, 2 mM glutamine, 0.11 mg/ml sodium pyruvate and 10% MCSF derived from 3T3-MCSF cell culture supernatants. Cells were maintained in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were resuspended in 1 ml of Trizol after 48 h of infection. 200 microliters of chloroform were added before centrifugation at 15,000 g for 10 min at 4°C. An equal volume of 70% ethanol was added to the aqueous layer, and RNA was extracted using silica spin columns (Invitrogen PureLink RNA Mini Kit). Purified RNA samples were treated with DNase (Purelink) and EDTA.
Gene expression profiling was carried out using a 3’ Tag-RNA-Seq protocol. Barcoded sequencing libraries were each prepared from 200 ng total RNA sample using the QuantSeq 3' mRNA-Seq Library Prep FWD kit for multiplexed sequencing, according to the recommendations of the manufacturer (Lexogen, Vienna, Austria). The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA). The libraries were quantified by fluorometry on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. The library pool was Exonuclease VII treated (NEB, Ipswich, MA), SPRI-bead purified with KapaPure beads (Kapa Biosystems/Roche, Basel, Switzerland), quantified via qPCR with a Kapa Library Quantification kit (Kapa Biosystems) on a QuantStudio5 RT-PCR system (Applied Biosystems, Foster City, CA). Libraries were sequenced on a NextSeq500 sequencer (Illumina, San Diego, CA) with single-end 85 bp reads.
3’ Tag-RNA-Seq (see: https://dnatech.genomecenter.ucdavis.edu/tag-seq-gene-expression-profiling/)

treatment_protocol: Macrophage monolayers were overlaid with M. tuberculosis suspensions and infected at a multiplicity of infection of 2 using a ‘spinfection protocol’ during which cells and bacteria were centrifuged for 10 min at 400 g. Cells were returned to regular macrophage media. Media was replaced daily until RNA harvest.

value: Bone-marrow derived macrophages

value: Atg7fl/fl LysMcre+/+

value: Mock infected


title: Atg7fl/fl LysMcre+/- macrophages, mock infected, biol rep 3

value: Atg7fl/fl LysMcre+/-


title: Healthy_control [PAD_15]


title: mutIAD [PAD_156_2019]


title: mutIAD [PAD_156_2012]


title: KFC S HY66


title: Atg16L1fl/fl LysMcre+/+ macrophages, mock infected, biol rep 3

value: Atg16L1fl/fl LysMcre+/+


title: F2G.1

value: Nucleus Accumbens

value: Female

value: Direct-zol RNA Microprep Kit (Zymo Research)


title: E326K/WT 1_DIV40

data_processing:
The sequencing data was analyzed with the Cell Ranger software (version 6.0.1) provided by 10x Genomics. Demultiplexing of the sequencing reads was performed with cellranger mkfastq.
For each sample, FASTQ files generated with cellranger mkfastq were subsequently processed with cellranger count. Cellranger count performs alignment, filtering, barcode counting and UMI counting. Using the filtered barcodes, it also generates feature-barcode matrices
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: cellranger output files for raw gene-barcode matrix ( barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz )

growth_protocol: Midbrain organoids were generated using a protocol developed in our group dapted from Jo et al., 2016

extract_protocol:
RNA libraries were prepared according to the standard 10X Genomics 3' Single Cell v2 protocol.
Cells loaded to Chromium Chip (target cell recovery): 10,000 cells. Library Preparation Kit: Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics). Sequencing parameters: NovaSeq 6000, SP Flow Cell, 100 cycles. Read 1: 28 bp, i7-index: 10 bp, i5-index 10 bp, Read 2: 90 bp. Q30 value: 91,88%

treatment_protocol: Midbrain organoids were dissociated into single-cell suspension following the Worthington Papain Dissociation System kit instructions (Worthington Biochemical) with intermittent trituration steps. The final solution was centrifuged 300g per 7 min, cell pellets were resuspended in PBS-0,04% BSA, and filtered twice (40um, 30um) to obtain single-cell suspensions.

value: E326K/WT Mutant


title: F2G.3


title: Atg16L1fl/fl LysMcre+/- macrophages, mock infected, biol rep 3

value: Atg16L1fl/fl LysMcre+/-


title: Atg7fl/fl macrophages, mock infected, biol rep 3


title: F2G.4


title: KFC L HY65

value: HY

value: KFC

value: L


title: F1R.5


title: E326K/WT 1 GC_DIV40

value: iPSC-derived midbrain organoids

value: Day 40 of differentiation

value: E326K/WT Gene corrected


title: KFC L HY64


title: KFC S HY63

value: S


title: L444P/L444P 2 - GC_DIV40

value: L444P/L444P 2 - Gene corrected


title: F1R.4


title: KFC S HY62


title: F1R.2


title: Atg16L1fl/fl macrophages, mock infected, biol rep 3

value: Bone-marrow derived macrophages


title: Atg5fl/fl LysMcre+/+ macrophages, mock infected, biol rep 3

value: Atg5fl/fl LysMcre+/+

value: Mock infected


title: Atg5fl/fl LysMcre+/- macrophages, mock infected, biol rep 3

value: Atg5fl/fl LysMcre+/-


title: Healthy_control [PAD_27]

value: Control

value: EBV-B


title: L444P/L444P 1 - GC_DIV60

value: Day 60 of differentiation

value: L444P/L444P 1 - Gene corrected


title: NF L HY59

value: NF


title: Atg5fl/fl macrophages, mock infected, biol rep 3


title: RNA-seq_DMSO_mut_3

data_processing:
mapping with Bowtie2 (version 2.3.4.1)
mapping with Bowtie2 (version 2.3.4.1)
Genome_build: hg19 from UCSC
Supplementary_files_format_and_content: bw and csv files were generated with featureCounts (version 2.0.1)

source_name: heart

extract_protocol:
Total RNA from iPSCMs was extracted using TRIzol reagents (Thermo Fisher Scientific)
NEBNext® UltraTM ll Directional RNA Library Prep Kit

value: iPS cardiomyocyte

tag: mutation

tag: name in supplementary file


title: Atg7fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 3

value: Atg7fl/fl LysMcre+/+

value: Infection with M. tuberculosis for 48h


title: RNA-seq_DMSO_mut_2


title: NF S HY58

tag: tissue

value: HY


title: NF L HY57

value: L


title: F1G.4

value: Nucleus Accumbens

value: Female

value: Direct-zol RNA Microprep Kit (Zymo Research)


title: F1G.5


title: RNA-seq_DMSO_mut_1


title: Atg7fl/fl macrophages, infected with M. tuberculosis, biol rep 3

value: Bone-marrow derived macrophages

tag: genotype


title: F1G.3


title: Atg16L1fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 3

value: Atg16L1fl/fl LysMcre+/+


title: Atg7fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 3

value: Atg7fl/fl LysMcre+/-


title: ISO S HY52

value: ISO

value: S


title: F1G.1


title: F1G.2


title: ISO L HY56


title: ISO S HY53


title: L444P/L444P 2_DIV40

value: iPSC-derived midbrain organoids

value: Day 40 of differentiation

value: L444P/L444P 2 Mutant


title: scATAC_WT_2

description: scATAC-seq

data_processing:
Cell Ranger software (ver 3.0.2, 10X Genomics)
Cell Ranger ATAC software (ver 1.2.0, 10X Genomics)
Genome_build: Cell Ranger mm10 reference genome
Supplementary_files_format_and_content: tsv files and mtx files from Cell Ranger and h5 files from Cell Ranger ATAC

extract_protocol:
Embryonic hearts of E17.5 were minced and enzymatically dissociated using the same digestion buffer as what used in the scRNA-seq analysis.
scATAC-seq targeting 3,000 cells per sample was performed using Chromium Single Cell ATAC Library and Gel Bead kit (10x Genomics) according to the manufacturer’s instruction. Libraries were sequenced on a NovaSeq 6000 System (Illumina) using a NovaSeq S4 Reagent Kit (200 cycles, 20027466, Illumina).

tag: day

value: embryonic day 17.5

value: WT


title: ISO S HY50


title: Atg16L1fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 3

value: Atg16L1fl/fl LysMcre+/-

tag: treatment


title: Atg16L1fl/fl macrophages, infected with M. tuberculosis, biol rep 3

value: Infection with M. tuberculosis for 48h


title: scATAC_WT_1

description: scATAC-seq


title: Atg5fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 3

value: Atg5fl/fl LysMcre+/+


title: KF S HY47

value: HY

value: KF


title: F1R.1

value: Nucleus Accumbens

value: Female


title: Atg5fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 3

value: Bone-marrow derived macrophages

value: Atg5fl/fl LysMcre+/-


title: acATAC_KI_1

description: scATAC-seq


title: KF S HY44


title: KF L HY48

value: L


title: RNA-seq_WT_4

value: iPS cardiomyocyte


title: RNA-seq_WT_3


title: RNA-seq_TT-10_mut_3


title: RNA-seq_TT-10_mut_2


title: RNA-seq_TT-10_mut_1


title: Atg5fl/fl macrophages, infected with M. tuberculosis, biol rep 3


title: RNA-seq_WT_1


title: RNA-seq_WT_2


title: RNA-seq_mut_4


title: Atg7fl/fl LysMcre+/+ macrophages, mock infected, biol rep 1

value: Atg7fl/fl LysMcre+/+

value: Mock infected


title: Atg7fl/fl LysMcre+/- macrophages, mock infected, biol rep 2

value: Atg7fl/fl LysMcre+/-


title: KF L HY41


title: scRNA_E17.5_WT_2

description: scRNA-seq

extract_protocol:
Embryonic hearts of E13.5 and E17.5 were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase, 1 mg/mL dispase, and 20 U/mL DNase I, with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer to remove the debris and multiplets, 5,000 cells were prepared to a concentration of 1000 cells/µL and loaded into the Chromium Controller.
single-cell cDNA libraries were generated using the Chromium 3’  v3 chemistry kit (10x Genomics) according to the manufacturer’s instruction. Libraries were sequenced on a NovaSeq 6000 System (Illumina) using a NovaSeq S4 Reagent Kit (200 cycles, 20027466, Illumina).


title: scRNA_E17.5_KI_1

description: scRNA-seq


title: NF S HY39

value: NF

value: S


title: RNA-seq_mut_3


title: scRNA_E17.5_WT_1

description: scRNA-seq

value: embryonic day 17.5

value: WT


title: RNA-seq_mut_2


title: scRNA_E17.5_KI_2

description: scRNA-seq


title: NF S HY37


title: RNA-seq_mut_1


title: KF S HY42


title: KF S HY36


title: scRNA_E13.5_WT_1

description: scRNA-seq

value: embryonic day 13.5


title: Atg16L1fl/fl LysMcre+/- macrophages, mock infected, biol rep 2

value: Atg16L1fl/fl LysMcre+/-


title: Fibrotic kidney allograft rep 6

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description:
isolated single nuclei - RNA
KUT100

data_processing:
Count matrices were generated using cellranger
Seurat objects were created using count matrices and the counts were normalized for library size
Seurat objects of normalized counts for all samples were integrated into one combined object
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of raw counts for each sample generated using cellranger

source_name: Kidney allograft

extract_protocol:
Single nuclei were isolated using Nuclei EZ lysis buffer with protease inhibitor. The homgenate was filtered with a 40um cell strainer and, then, centrifuged at low speed. The nuclei pellet was resuspended in Nuclei resuspspension buffer and passed through the 40um filter.
Libraries were prepared according to standard 10x Genomics and Illumina instructions. Libraries were generated using the 10x 5' Gene Expression kit.
Single nuclei RNA-seq (10x genomics platform)

tag: group

value: Fibrotic kidney allograft

tag: est. conc. of cells

tag: mean reads per cells

tag: fraction of reads mapped to genome (%)


title: Atg16L1fl/fl macrophages, mock infected, biol rep 2


title: scRNA_E13.5_WT_2

first: Shintaro

last: Yamada

description: scRNA-seq

tag: strain


title: scRNA_E13.5_KI_1

description: scRNA-seq


title: Fibrotic kidney allograft rep 5

description:
isolated single nuclei - RNA
KUT088


title: KF S HY34

value: HY

tag: social treatment

value: KF

tag: injection treatment


title: Atg5fl/fl LysMcre+/+ macrophages, mock infected, biol rep 2

tag: cell type

value: Atg5fl/fl LysMcre+/+


title: KF L HY33


title: scRNA_E13.5_KI_2

description: scRNA-seq


title: Atg5fl/fl LysMcre+/- macrophages, mock infected, biol rep 2

value: Bone-marrow derived macrophages


title: Atg7fl/fl macrophages, mock infected, biol rep 2


title: Fibrotic kidney allograft rep 2

description:
isolated single nuclei - RNA
KUT056


title: KF L HY32


title: Fibrotic kidney allograft rep 3

description:
isolated single nuclei - RNA
KUT065


title: Atg5fl/fl macrophages, mock infected, biol rep 2


title: scRNA_E17.5_KI_3

description: scRNA-seq


title: KF S HY31


title: KF L HY30


title: Atg7fl/fl LysMcre+/+ macrophages, infected with M. tuberculosis, biol rep 2

value: Infection with M. tuberculosis for 48h


title: Fibrotic kidney allograft rep 1

description:
isolated single nuclei - RNA
KUT040


title: Atg16L1fl/fl LysMcre+/+ macrophages, mock infected, biol rep 2

value: Atg16L1fl/fl LysMcre+/+


title: Atg7fl/fl LysMcre+/- macrophages, infected with M. tuberculosis, biol rep 2


title: KF L HY35

value: L


title: Normal kidney allograft rep 3

description:
isolated single nuclei - RNA
KUT081

value: Normal kidney allograft


title: NF S HY28


title: Fibrotic kidney allograft rep 4

description:
isolated single nuclei - RNA
KUT076


title: Normal kidney allograft rep 2

description:
isolated single nuclei - RNA
KUT060