title: pan_tissue_SpinalCord_KO

description:
Library name: pan_tissue_SpinalCord_KO_scATAC-seq
UUATAC-seq

value: SpinalCord


title: P+9216 (P_9216_AR_Plate6)

status: Public on Jul 31 2026

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description: Library name: P_and_9216_P_9216_AR_Plate6

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)  The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.         The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates.      Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files. Tab-delimited files (HIC files) describing the chromatin contacts will be generated with in-house developing package using the filtered BAM files.
Assembly: hg38
Supplementary files format and content: An ALLC file contains 7 columns with DNA methylation information of a single cell at single base resolution. The columns are 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.   A contact file contains long range chromatin contacts of a single cell after removing the ones overlapping blacklists. The columns are 1. Strand1, 2. Chromosome1, 3. Position1, 4. place holder column, always be 0, 5. Strand2, 6. Chromosome2, 7. Position2, 8. place holder column, always be 1.
Library strategy: snm3C-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Placenta

extract_protocol:
Nuclei extraction protocol can be found at https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1
Library preparation protocol can be found at https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1

tag: tissue

value: Placenta


title: cDC1, Clec1a WT1_n4_necrocoli

city: Nantes

first: Elise

last: Chiffoleau

address: 30 Bd jean Monnet CHU

country: France

description:
Library name: Sample 139
TO240_DGEseq.unq.refseq.umi.dat

library_source: transcriptomic

data_processing:
An average of 5 million 75 bp single-end reads were obtained for each sample.
Samples were demultiplexed and aligned to the GRCm38 (mm10) genome using the DGE bioinformatics pipeline.
Post-sequencing, data demultiplexing was performed using Illumina bcl2fastq.
The resulting FASTQ files were analyzed using the 3’ Sequencing RNA Profiling (SRP) pipeline
Assembly: mm10
Supplementary files format and content: Digital gene expression (DGE) profiles were generated by counting the number of unique UMIs associated with each RefSeq gene for each sample and expressed in .dat format

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
5,000 cells were incubated in lysis buffer containing 0.16uL 10% Triton X-100, 0.08 uL RNAse Out (40U/µL, Invitrogen) and 3.75 µL RNAse DNAse free water
Lyzed cells were loaded on a 96-plate using an OT-2 library prep robot (Opentrons). 1uL barcoded RT-primers with universal adapters, well-specific barcodes, and unique molecular identifiers were then added to the wells and incubated at 72°C for 3 min before reverse transcription. Barcoded complementary DNAs from multiple samples were then pooled, amplified, and tagmented using a transposon fragmentation approach which enriches for 3′ ends of complementary DNA.

treatment_protocol: Spleen from WT and Clec1a KO mice were recovered, minced and incubated with collagenase IV for 45 minutes at 37°C (Roche, cat: 11088882001). The resulting cell suspension was then enriched in cDC1s by incubation with a DC isolation kit (Milteny, cat: 130-091-169) and sorted with an AutoMACS separator. The resulting cell suspension was then stained with fluorochrome-conjugated antibodies and purified cDC1s were sorted by FACS (based on the expression of CD11c, MHC-II and XCR1) using a Cytek Aurora spectral flow cytometer. Purified cDC1s were then plated in flat-bottom 96-well plates and stimulated with E. coli (MOI = 10), MCA-OVA UV-treated cells (ratio 1:10) or recombinant mouse IFNβ (1000 U/ml, BioTechne R&D Systems cat: 8234-MB-010) for 6h. Then, cells were extensively washed and harvested for RNAseq experiments.

value: spleen

tag: strain

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

tag: age

value: 8-12 weeks old

tag: cell type

value: type 1 conventional dendritic cells

tag: genotype

value: Clec1a WT

tag: treatment

value: stimulated with necrotic cells plus E Coli

tag: time


title: pan_tissue_SmallIntestine_KO

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

description:
Library name: pan_tissue_SmallIntestine_KO_scATAC-seq
UUATAC-seq

library_source: genomic single cell

data_processing:
Raw FASTQ files were split by i7 indexes of DNBSEQ-T7 using splitBarcode (v0.1.6) then converted to BAM format. The 30-bp barcodes were tagged and reads with low quality were removed. Barcodes were next corrected and combined with the i7 indexes to label cells. The barcode-corrected BAM files were split by barcode 3 which label samples. Cell barcodes (i7 indexes + 30-bp barcodes) were added to the query name of each read. BAM files were then converted to FASTQ files with 30-bp barcodes and reverse complementary mosaic end (ME) sequences trimmed. Reads were aligned to mm10 using BWA (version 0.7.15) in paired-end mode. The aligned and sorted BAM files were shifted using the alignmentSieve function in deepTools (version 3.5.1) to correct the 9-bp gap. The shifted BAM files were next merged per sample and converted to BEDPE files (BED format). BEDPE files were cleaned to fragment files for subsequent analyses.
Assembly: mm10
Supplementary files format and content: Compressed BED  files containing sorted fragments
Supplementary files format and content: Compressed Tab-delimited text files containing metadata of cells analyzed

source_name: SmallIntestine

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Library preparations were performed with the UUATAC-seq protocol

value: SmallIntestine

value: Mecp2 KO

tag: Sex

value: Male

value: 9 weeks

tag: mouse id


title: pan_tissue_Prostate_KO

description:
Library name: pan_tissue_Prostate_KO_scATAC-seq
UUATAC-seq

source_name: Prostate

value: Prostate


title: pan_tissue_Pituitary_KO

description:
Library name: pan_tissue_Pituitary_KO_scATAC-seq
UUATAC-seq

source_name: Pituitary

value: Pituitary


title: P+9213 (P_9213_AR_Plate2)

description: Library name: P_and_9213_P_9213_AR_Plate2


title: cDC1, Clec1a WT1_n4_necro

description:
Library name: Sample 138
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: pan_tissue_Pancreas_KO

description:
Library name: pan_tissue_Pancreas_KO_scATAC-seq
UUATAC-seq

source_name: Pancreas

value: Pancreas


title: neural_BrainStem_KO_rep3

description:
Library name: neural_BrainStem_KO_rep3_scATAC-seq
UUATAC-seq

source_name: BrainStem

value: BrainStem


title: P+9213 (P_9213_AR_Plate1)

description: Library name: P_and_9213_P_9213_AR_Plate1


title: pan_tissue_Muscle_KO

description:
Library name: pan_tissue_Muscle_KO_scATAC-seq
UUATAC-seq

source_name: Muscle

value: Muscle


title: cDC1, Clec1a WT1_n4_ifn

description:
Library name: Sample 137
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with type I IFN


title: Cerebellum_KO_rep2

description:
Library name: Cerebellum_KO_rep2_scRNA-seq
UURNA-seq

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were split by i7 indexes of DNBSEQ-T7 using splitBarcode (v0.1.6) then converted to BAM format. The 30-bp cell barcodes and 7-bp unique molecular identifiers (UMIs) were extracted and tagged. Reads with poor barcode or UMI quality (more than 8/37 bases showing quality < 10) were tagged with XQ and removed afterwards. The known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each barcode or UMI. The corrected BAM files were converted to FASTQ files with barcodes and UMIs trimmed. Cutadapt was then used to trim poly-A. Before Read-2 files were used for alignment, seqtk was performed to reverse the sequences. Reads were aligned to mm10 using STAR in single-end mode. The aligned BAM files were then merged with the unaligned ones to recover barcode and UMI information. The TagReadWithGeneExon function was employed to recognize reads mapped to the exonic and intronic regions of genes. Then the tagged BAM files were split by the third 10-bp barcodes (barcode 3) of each read, which is designed to distinguish different samples. BAM files with different i7 indexes were all merged if they shared the same barcode 3. Finally, the top 20,000 barcodes in each BAM file were extracted and their expression matrices were quantified.
Assembly: mm10
Supplementary files format and content: Compressed Tab-delimited text files containing gene expression matrices
Supplementary files format and content: Compressed Tab-delimited text files containing metadata of cells analyzed

molecule: nuclear RNA

source_name: Cerebellum

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Library preparations were performed with the UURNA-seq protocol

value: Cerebellum

value: 7 weeks


title: cDC1, Clec1a WT2_n2_ifn

description:
Library name: Sample 147
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old


title: NTb+PT-1LVAN (NTb_CP2V6_AR_Plate5)

description: Library name: NTb_and_PT-1LVAN_NTb_CP2V6_AR_Plate5

source_name: Tibial Nerve

value: Tibial Nerve


title: pan_tissue_Lung_KO

description:
Library name: pan_tissue_Lung_KO_scATAC-seq
UUATAC-seq

source_name: Lung

value: Lung


title: pan_tissue_LymphNode_KO

description:
Library name: pan_tissue_LymphNode_KO_scATAC-seq
UUATAC-seq

source_name: LymphNode

value: LymphNode

value: Mecp2 KO


title: cDC1, Clec1a WT1_n4_ecoli

description:
Library name: Sample 136
TO240_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: Clec1a WT

value: stimulated with E Coli


title: NTb+PT-1LVAN (NTb_CP2V6_AR_Plate4)

description: Library name: NTb_and_PT-1LVAN_NTb_CP2V6_AR_Plate4


title: pan_tissue_LargeIntestine_KO

description:
Library name: pan_tissue_LargeIntestine_KO_scATAC-seq
UUATAC-seq

source_name: LargeIntestine

value: LargeIntestine

value: Male

value: 9 weeks


title: pan_tissue_Kidney_KO

description:
Library name: pan_tissue_Kidney_KO_scATAC-seq
UUATAC-seq

source_name: Kidney

value: Kidney


title: cDC1, Clec1a WT1_n3_ns

description:
Library name: Sample 135
TO240_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: pan_tissue_Liver_KO

description:
Library name: pan_tissue_Liver_KO_scATAC-seq
UUATAC-seq

source_name: Liver

value: Liver


title: NTb+PT-1LVAN (NTb_CP2V6_AR_Plate3)

description: Library name: NTb_and_PT-1LVAN_NTb_CP2V6_AR_Plate3


title: pan_tissue_Heart_KO

description:
Library name: pan_tissue_Heart_KO_scATAC-seq
UUATAC-seq

source_name: Heart

value: Heart


title: cDC1, Clec1a WT1_n3_necrocoli

description:
Library name: Sample 134
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells plus E Coli


title: pan_tissue_Eye_KO

description:
Library name: pan_tissue_Eye_KO_scATAC-seq
UUATAC-seq

source_name: Eye

value: Eye


title: NTb+PT-1LVAN (NTb_CP2V6_AR_Plate2)

description: Library name: NTb_and_PT-1LVAN_NTb_CP2V6_AR_Plate2

value: Tibial Nerve


title: P+9213 (P_9213_AR_Plate7)

description: Library name: P_and_9213_P_9213_AR_Plate7

source_name: Placenta

value: Placenta


title: pan_tissue_Epididymis_KO

description:
Library name: pan_tissue_Epididymis_KO_scATAC-seq
UUATAC-seq

source_name: Epididymis

value: Epididymis


title: pan_tissue_Diencephalon_KO

description:
Library name: pan_tissue_Diencephalon_KO_scATAC-seq
UUATAC-seq

source_name: Diencephalon

value: Diencephalon

value: Mecp2 KO


title: cDC1, Clec1a WT1_n3_necro

description:
Library name: Sample 133
TO240_DGEseq.unq.refseq.umi.dat

source_name: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Clec1a WT

value: stimulated with necrotic cells


title: pan_tissue_Cerebellum_KO

description:
Library name: pan_tissue_Cerebellum_KO_scATAC-seq
UUATAC-seq

value: Cerebellum

value: Male

value: 9 weeks


title: NTb+PT-1LVAN (NTb_CP2V6_AR_Plate1)

description: Library name: NTb_and_PT-1LVAN_NTb_CP2V6_AR_Plate1


title: cDC1, Clec1a WT1_n3_ifn

description:
Library name: Sample 132
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with type I IFN


title: pan_tissue_Thyroid_KO

description:
Library name: pan_tissue_Thyroid_KO_scATAC-seq
UUATAC-seq

source_name: Thyroid

value: Thyroid


title: pan_tissue_BrownFat_KO

description:
Library name: pan_tissue_BrownFat_KO_scATAC-seq
UUATAC-seq

source_name: BrownFat

value: BrownFat


title: pan_tissue_BrainStem_KO

description:
Library name: pan_tissue_BrainStem_KO_scATAC-seq
UUATAC-seq

source_name: BrainStem

value: BrainStem


title: cDC1, Clec1a WT1_n3_ecoli

description:
Library name: Sample 131
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with E Coli


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate9)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate9

value: Tibial Nerve


title: pan_tissue_Thymus_KO

description:
Library name: pan_tissue_Thymus_KO_scATAC-seq
UUATAC-seq

source_name: Thymus

value: Thymus


title: pan_tissue_BoneMarrow_KO

description:
Library name: pan_tissue_BoneMarrow_KO_scATAC-seq
UUATAC-seq

source_name: BoneMarrow

value: BoneMarrow

value: Mecp2 KO


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate8)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate8

source_name: Tibial Nerve


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate7)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate7


title: cDC1, Clec1a WT1_n2_ns

description:
Library name: Sample 130
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: Non stimulated


title: pan_tissue_Bladder_KO

description:
Library name: pan_tissue_Bladder_KO_scATAC-seq
UUATAC-seq

source_name: Bladder

value: Bladder


title: pan_tissue_AdrenalGland_KO

description:
Library name: pan_tissue_AdrenalGland_KO_scATAC-seq
UUATAC-seq

source_name: AdrenalGland

value: AdrenalGland


title: C57_WhiteFat_WT_Male5

description:
Library name: C57_WhiteFat_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

molecule: polyA RNA

source_name: WhiteFat

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: WhiteFat

value: WT

value: Male

value: 8 weeks


title: cDC1, Clec1a WT1_n2_necrocoli

description:
Library name: Sample 129
TO240_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: Clec1a WT

value: stimulated with necrotic cells plus E Coli


title: C57_WhiteFat_WT_Male4

description:
Library name: C57_WhiteFat_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate6)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate6


title: C57_WhiteFat_WT_Male3

description:
Library name: C57_WhiteFat_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT1_n2_necro

description:
Library name: Sample 128
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells


title: C57_WhiteFat_WT_Female3

description:
Library name: C57_WhiteFat_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate5)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate5

value: Tibial Nerve


title: C57_WhiteFat_WT_Male2

description:
Library name: C57_WhiteFat_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: cDC1, Clec1a WT1_n2_ifn

description:
Library name: Sample 127
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: stimulated with type I IFN


title: C57_WhiteFat_WT_Female1

description:
Library name: C57_WhiteFat_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_WhiteFat_KO_Male5

description:
Library name: C57_WhiteFat_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: C57_WhiteFat_WT_Female2

description:
Library name: C57_WhiteFat_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WhiteFat

value: WT


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate4)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate4


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate3)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate3


title: C57_WhiteFat_KO_Male4

description:
Library name: C57_WhiteFat_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 8 weeks


title: cDC1, Clec1a WT1_n1_ns

description:
Library name: Sample 125
TO240_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: Clec1a WT

value: Non stimulated


title: C57_WhiteFat_KO_Male2

description:
Library name: C57_WhiteFat_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate2)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate2


title: cDC1, Clec1a WT1_n1_necrocoli

description:
Library name: Sample 124
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells plus E Coli


title: C57_WhiteFat_KO_Male1

description:
Library name: C57_WhiteFat_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_WhiteFat_KO_Female3

description:
Library name: C57_WhiteFat_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: cDC1, Clec1a WT1_n1_necro

description:
Library name: Sample 123
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with necrotic cells


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate10)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate10

value: Tibial Nerve


title: C57_WhiteFat_KO_Female1

description:
Library name: C57_WhiteFat_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: NTb+PT-1K2DA (NTb_CHLWU_AR_Plate1)

description: Library name: NTb_and_PT-1K2DA_NTb_CHLWU_AR_Plate1


title: neural_SpinalCord_KO_rep3

description:
Library name: neural_SpinalCord_KO_rep3_scATAC-seq
UUATAC-seq

source_name: SpinalCord

value: SpinalCord


title: C57_WhiteFat_KO_Female2

description:
Library name: C57_WhiteFat_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WhiteFat

value: 8 months


title: C57_Uterus_WT_Female4

description:
Library name: C57_Uterus_WT_Female4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Uterus

value: Uterus

value: WT

value: 4.7 months


title: cDC1, Clec1a WT1_n2_ecoli

description:
Library name: Sample 126
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Clec1a WT

value: stimulated with E Coli


title: C57_Uterus_WT_Female2

description:
Library name: C57_Uterus_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT1_n1_ifn

description:
Library name: Sample 122
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with type I IFN


title: M1C+H1930002 (M1C_presorted_002_Plate8)

description: Library name: M1C_and_H1930002_M1C_presorted_002_Plate8

source_name: Primary Motor Cortex

value: Primary Motor Cortex


title: C57_Uterus_WT_Female1

description:
Library name: C57_Uterus_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 8 weeks


title: cDC1, Clec1a WT1_n1_ecoli

description:
Library name: Sample 121
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates


title: M1C+H1930002 (M1C_presorted_002_Plate7)

description: Library name: M1C_and_H1930002_M1C_presorted_002_Plate7


title: C57_Uterus_KO_Female3

description:
Library name: C57_Uterus_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7.5 months


title: C57_Uterus_KO_Female2

description:
Library name: C57_Uterus_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO2_n4_ns

description:
Library name: Sample 120
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: Non stimulated


title: C57_Uterus_KO_Female1

description:
Library name: C57_Uterus_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Uterus

value: 9 weeks


title: C57_Thyroid_WT_Male5

description:
Library name: C57_Thyroid_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Thyroid

value: WT

value: Male


title: M1C+H1930002 (M1C_presorted_002_Plate6)

description: Library name: M1C_and_H1930002_M1C_presorted_002_Plate6


title: C57_Thyroid_WT_Male4

description:
Library name: C57_Thyroid_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO2_n4_necro

description:
Library name: Sample 118
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells


title: C57_Thyroid_WT_Male2

description:
Library name: C57_Thyroid_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: M1C+H1930002 (M1C_presorted_002_Plate4)

description: Library name: M1C_and_H1930002_M1C_presorted_002_Plate4

value: Primary Motor Cortex


title: cDC1, Clec1a KO2_n4_ifn

description:
Library name: Sample 117
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with type I IFN


title: C57_Thyroid_WT_Female2

description:
Library name: C57_Thyroid_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female


title: C57_Thyroid_WT_Female3

description:
Library name: C57_Thyroid_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO2_n4_ecoli

description:
Library name: Sample 116
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with E Coli


title: M1C+H1930002 (M1C_presorted_002_Plate3)

description: Library name: M1C_and_H1930002_M1C_presorted_002_Plate3


title: M1C+H1930002 (M1C_presorted_002_Plate2)

description: Library name: M1C_and_H1930002_M1C_presorted_002_Plate2


title: C57_Thyroid_KO_Male2

description:
Library name: C57_Thyroid_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: cDC1, Clec1a KO2_n3_ns

description:
Library name: Sample 115
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: Non stimulated


title: C57_Thyroid_KO_Female1

description:
Library name: C57_Thyroid_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: cDC1, Clec1a KO2_n3_necrocoli

description:
Library name: Sample 114
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells plus E Coli


title: M1C+H1930002 (M1C_3C_002_Plate8)

description: Library name: M1C_and_H1930002_M1C_3C_002_Plate8


title: C57_Thymus_WT_Male6

description:
Library name: C57_Thymus_WT_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Thymus

value: WT


title: C57_Thymus_WT_Male5

description:
Library name: C57_Thymus_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 8 weeks


title: M1C+H1930002 (M1C_3C_002_Plate7)

description: Library name: M1C_and_H1930002_M1C_3C_002_Plate7


title: C57_Thymus_WT_Male4

description:
Library name: C57_Thymus_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO2_n3_ifn

description:
Library name: Sample 112
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells


title: C57_Thymus_WT_Male2

description:
Library name: C57_Thymus_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: C57_Thymus_WT_Female3

description:
Library name: C57_Thymus_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7.5 months


title: M1C+H1930002 (M1C_3C_002_Plate6)

description: Library name: M1C_and_H1930002_M1C_3C_002_Plate6

value: Primary Motor Cortex


title: C57_Thymus_WT_Female2

description:
Library name: C57_Thymus_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female


title: C57_Thymus_WT_Female1

description:
Library name: C57_Thymus_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO2_n2_ns

description:
Library name: Sample 110
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates


title: C57_Thymus_KO_Male4

description:
Library name: C57_Thymus_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: cDC1, Clec1a KO2_n2_necrocoli

description:
Library name: Sample 109
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO


title: C57_Thymus_KO_Male2

description:
Library name: C57_Thymus_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: M1C+H1930002 (M1C_3C_002_Plate3)

description: Library name: M1C_and_H1930002_M1C_3C_002_Plate3


title: C57_Thymus_KO_Male1

description:
Library name: C57_Thymus_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: cDC1, Clec1a KO2_n2_necro

description:
Library name: Sample 108
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: C57_Thymus_KO_Female3

description:
Library name: C57_Thymus_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: M1C+H1930002 (M1C_3C_002_Plate2)

description: Library name: M1C_and_H1930002_M1C_3C_002_Plate2


title: C57_Thymus_KO_Female2

description:
Library name: C57_Thymus_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: cDC1, Clec1a KO2_n2_ifn

description:
Library name: Sample 107
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with type I IFN


title: C57_Testis_WT_Male5

description:
Library name: C57_Testis_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Testis

value: Testis

value: WT


title: M1C+H1930002 (M1C_3C_002_Plate1)

description: Library name: M1C_and_H1930002_M1C_3C_002_Plate1


title: M1C+H1930001 (M1C_presorted_001_Plate8)

description: Library name: M1C_and_H1930001_M1C_presorted_001_Plate8


title: cDC1, Clec1a KO2_n2_ecoli

description:
Library name: Sample 106
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: C57_Testis_WT_Male3

description:
Library name: C57_Testis_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 8 weeks


title: C57_Testis_WT_Male2

description:
Library name: C57_Testis_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: cDC1, Clec1a KO2_n1_ns

description:
Library name: Sample 105
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Non stimulated


title: C57_Testis_KO_Male5

description:
Library name: C57_Testis_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_Testis_KO_Male4

description:
Library name: C57_Testis_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: M1C+H1930001 (M1C_presorted_001_Plate7)

description: Library name: M1C_and_H1930001_M1C_presorted_001_Plate7

value: Primary Motor Cortex


title: cDC1, Clec1a KO2_n1_necrocoli

description:
Library name: Sample 104
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with necrotic cells plus E Coli


title: C57_Testis_KO_Male2

description:
Library name: C57_Testis_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 9 weeks


title: C57_Testis_KO_Male1

description:
Library name: C57_Testis_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: cDC1, Clec1a KO2_n1_necro

description:
Library name: Sample 103
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: stimulated with necrotic cells


title: M1C+H1930001 (M1C_presorted_001_Plate6)

description: Library name: M1C_and_H1930001_M1C_presorted_001_Plate6


title: C57_Telencephalon_WT_Male5

description:
Library name: C57_Telencephalon_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Telencephalon

value: Telencephalon

value: WT


title: M1C+H1930001 (M1C_presorted_001_Plate5)

description: Library name: M1C_and_H1930001_M1C_presorted_001_Plate5


title: C57_Telencephalon_WT_Male4

description:
Library name: C57_Telencephalon_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male


title: cDC1, Clec1a KO2_n1_ifn

description:
Library name: Sample 102
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with type I IFN


title: C57_Uterus_KO_Female4

description:
Library name: C57_Uterus_KO_Female4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Uterus

value: Female

value: 4.7 months


title: C57_Telencephalon_WT_Male3

description:
Library name: C57_Telencephalon_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: cDC1, Clec1a KO2_n4_necrocoli

description:
Library name: Sample 119
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells


title: C57_Testis_WT_Male4

description:
Library name: C57_Testis_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Testis


title: M1C+H1930002 (M1C_presorted_002_Plate5)

description: Library name: M1C_and_H1930002_M1C_presorted_002_Plate5

value: Primary Motor Cortex


title: M1C+H1930001 (M1C_presorted_001_Plate4)

description: Library name: M1C_and_H1930001_M1C_presorted_001_Plate4


title: C57_Telencephalon_WT_Male2

description:
Library name: C57_Telencephalon_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: cDC1, Clec1a KO2_n1_ecoli

description:
Library name: Sample 101
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with E Coli


title: C57_Telencephalon_WT_Female3

description:
Library name: C57_Telencephalon_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7.5 months


title: M1C+H1930001 (M1C_presorted_001_Plate3)

description: Library name: M1C_and_H1930001_M1C_presorted_001_Plate3


title: C57_Telencephalon_WT_Female2

description:
Library name: C57_Telencephalon_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Telencephalon


title: cDC1, Clec1a KO1_n4_ns

description:
Library name: Sample 100
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: Non stimulated


title: C57_Thyroid_KO_Male4

description:
Library name: C57_Thyroid_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Thyroid

value: Mecp2 KO

value: Male


title: C57_Telencephalon_WT_Female1

description:
Library name: C57_Telencephalon_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WT

value: Female


title: M1C+H1930001 (M1C_presorted_001_Plate2)

description: Library name: M1C_and_H1930001_M1C_presorted_001_Plate2


title: C57_Telencephalon_KO_Male5

description:
Library name: C57_Telencephalon_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: C57_Thyroid_KO_Female3

description:
Library name: C57_Thyroid_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: M1C+H1930002 (M1C_presorted_002_Plate1)

description: Library name: M1C_and_H1930002_M1C_presorted_002_Plate1


title: cDC1, Clec1a KO1_n4_necrocoli

description:
Library name: Sample 99
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells plus E Coli


title: C57_Telencephalon_KO_Male4

description:
Library name: C57_Telencephalon_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: M1C+H1930001 (M1C_presorted_001_Plate1)

description: Library name: M1C_and_H1930001_M1C_presorted_001_Plate1

value: Primary Motor Cortex


title: C57_Thyroid_KO_Male5

description:
Library name: C57_Thyroid_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: umbilical cord plasma, Gen3G, PubM2783

city: Sherbrooke

first: Luigi

last: Bouchard

country: Canada

institute: Université de Shebrooke

description: Library name: Gen3G_UCP_PubM2783

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with the FASTX-Toolkit integrated in the exceRpt pipeline. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using the STAR alignment algorithm version 2.4.2a.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple samples (PMID : 30956140).
Assembly: GRCh37
Supplementary files format and content: Comma-seperated value file, include non-normalized read counts for each microRNA detected in each samples.

source_name: umilical cord plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from up to 500 μL of UCP (130 µL to 500 µL, based on availability) kept at -80 °C until extraction. Prior to extraction, a volume of miRNeasy Serum/Plasma  Caenorhabditis elegans cel-miR-39-3p mimic Spike-In Control (Qiagen, catalog # 219610) was added to each sample, folowing a 1 μL for each 250 μL of plasma ratio. Elution of total RNA was performed in 75 µL of nuclease-free water, and 70 µL of this RNA eluate was then precipitated, dried and resuspended in 5 μL of nuclease-free water as previously described (PMID: 35246451). The whole volume was used for library preparation.
Samples were randomized before library preparation. The libraries were created using the the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) following  the standard procedure adapted to samples of low RNA concentration by Burgos et al (PMID: 23525801). To maintain an optimal reaction ratio, half of the reagents volumes were used for RNA ligation with adapters at 3′ and 5′ ends, reverse transcription, barcoding (index 1-48: one index per sample) and PCR amplification (15 cycles). Libraries were purified by migration in a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, Waltham, United States, catalog #EC265BOX). Fragments between 145 and 160 bp were excised and eluted from the gel with 300 µL of nuclease-free water at room temperature, during an overnight incubation at 500 RPM on a microplate shaker (VWR, ON, Canada, catalog #12620-930). Libraries were concentrated by precipitation following manufacturer's instructions, briefly with a 30 minutes incubation at -80°C, and resuspended in 25 µL of 10 mM Tris-HCl pH 8.5 buffer. Libraries sequencing, including quality control and sample pooling, was performed at the Centre d’expertise et de services Génome Québec (Montréal, Canada). The Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) was used to assess the quality of each library (i.e., concentration, library length and primer dimers absence).  Librairies were pooled equimolarly (200 pM final molarity; 48 libraries with different indexes per lane), denatured and clustered on an Illumina NovaSeq S1 flowcell following the Xp protocol from manufacturer’s recommendations. The sequencing run was performed for 100 cycles in single-end mode, on a NovaSeq 6000 platform.

value: umilical cord plasma

tag: fetal sex

value: female

tag: gestational age_at_birth_(weeks)

tag: delivery type

value: vaginal

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: C57_Telencephalon_KO_Male2

description:
Library name: C57_Telencephalon_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

tag: tissue

value: Telencephalon

tag: genotype

tag: strain

tag: age

value: 9 weeks


title: cDC1, Clec1a KO1_n4_necro

description:
Library name: Sample 98
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

tag: cell type

value: Clec1a KO

tag: treatment

value: stimulated with necrotic cells

tag: time


title: C57_Thyroid_KO_Female2

description:
Library name: C57_Thyroid_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Thyroid

value: Mecp2 KO

tag: Sex

value: 8 months

tag: mouse id


title: cDC1, Clec1a KO2_n3_necro

description:
Library name: Sample 113
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old


title: C57_Telencephalon_KO_Male1

description:
Library name: C57_Telencephalon_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 7 weeks


title: M1C+H1930001 (M1C_3C_001_Plate8)

description: Library name: M1C_and_H1930001_M1C_3C_001_Plate8


title: C57_Telencephalon_KO_Female3

description:
Library name: C57_Telencephalon_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: cDC1, Clec1a KO1_n4_ifn

description:
Library name: Sample 97
TO240_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: stimulated with type I IFN


title: M1C+H1930001 (M1C_3C_001_Plate7)

description: Library name: M1C_and_H1930001_M1C_3C_001_Plate7

value: Primary Motor Cortex


title: C57_Telencephalon_KO_Female2

description:
Library name: C57_Telencephalon_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Telencephalon


title: cDC1, Clec1a KO1_n4_ecoli

description:
Library name: Sample 96
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: C57_Stomach_WT_Male5

description:
Library name: C57_Stomach_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Stomach

value: Stomach

value: WT

value: 8 weeks


title: C57_Stomach_WT_Male4

description:
Library name: C57_Stomach_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: M1C+H1930001 (M1C_3C_001_Plate6)

description: Library name: M1C_and_H1930001_M1C_3C_001_Plate6


title: cDC1, Clec1a KO1_n3_ns

description:
Library name: Sample 95
TO240_DGEseq.unq.refseq.umi.dat

source_name: spleen

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: Clec1a KO

value: Non stimulated


title: M1C+H1930001 (M1C_3C_001_Plate5)

description: Library name: M1C_and_H1930001_M1C_3C_001_Plate5


title: C57_Stomach_WT_Male3

description:
Library name: C57_Stomach_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_Telencephalon_KO_Female1

description:
Library name: C57_Telencephalon_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 9 weeks


title: C57_Stomach_WT_Male2

description:
Library name: C57_Stomach_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 10 weeks


title: cDC1, Clec1a KO1_n3_necrocoli

description:
Library name: Sample 94
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: stimulated with necrotic cells plus E Coli


title: C57_Stomach_WT_Female3

description:
Library name: C57_Stomach_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: cDC1, Clec1a KO2_n3_ecoli

description:
Library name: Sample 111
TO240_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells


title: M1C+H1930001 (M1C_3C_001_Plate4)

description: Library name: M1C_and_H1930001_M1C_3C_001_Plate4

value: Primary Motor Cortex


title: C57_Stomach_WT_Female1

description:
Library name: C57_Stomach_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Stomach


title: cDC1, Clec1a KO1_n3_necro

description:
Library name: Sample 93
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: C57_Stomach_KO_Male5

description:
Library name: C57_Stomach_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: M1C+H1930001 (M1C_3C_001_Plate3)

description: Library name: M1C_and_H1930001_M1C_3C_001_Plate3


title: M1C+H1930002 (M1C_3C_002_Plate5)

description: Library name: M1C_and_H1930002_M1C_3C_002_Plate5


title: C57_Stomach_KO_Male4

description:
Library name: C57_Stomach_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: cDC1, Clec1a KO1_n3_ifn

description:
Library name: Sample 92
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with type I IFN


title: C57_Stomach_KO_Male2

description:
Library name: C57_Stomach_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: M1C+H1930001 (M1C_3C_001_Plate2)

description: Library name: M1C_and_H1930001_M1C_3C_001_Plate2


title: cDC1, Clec1a KO1_n3_ecoli

description:
Library name: Sample 91
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: stimulated with E Coli


title: C57_Stomach_KO_Female3

description:
Library name: C57_Stomach_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_Stomach_KO_Female2

description:
Library name: C57_Stomach_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: M1C+H1930001 (M1C_3C_001_Plate1)

description: Library name: M1C_and_H1930001_M1C_3C_001_Plate1


title: C57_Stomach_KO_Female1

description:
Library name: C57_Stomach_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: C57_Spleen_WT_Male6

description:
Library name: C57_Spleen_WT_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Spleen

value: Spleen

value: WT

value: Male


title: LV+STL003 (LV_STL003_AR_Plate8)

description: Library name: LV_and_STL003_LV_STL003_AR_Plate8

source_name: Left Ventricle

value: Left Ventricle


title: C57_Spleen_WT_Male5

description:
Library name: C57_Spleen_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO1_n2_necrocoli

description:
Library name: Sample 89
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells plus E Coli


title: C57_Spleen_WT_Male3

description:
Library name: C57_Spleen_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: LV+STL003 (LV_STL003_AR_Plate7)

description: Library name: LV_and_STL003_LV_STL003_AR_Plate7


title: cDC1, Clec1a KO1_n2_necro

description:
Library name: Sample 88
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: LV+STL003 (LV_STL003_AR_Plate6)

description: Library name: LV_and_STL003_LV_STL003_AR_Plate6


title: C57_Spleen_WT_Female2

description:
Library name: C57_Spleen_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: C57_Spleen_WT_Female3

description:
Library name: C57_Spleen_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO1_n2_ifn

description:
Library name: Sample 87
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates


title: C57_Spleen_WT_Female1

description:
Library name: C57_Spleen_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: cDC1, Clec1a KO1_n2_ecoli

description:
Library name: Sample 86
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO


title: LV+STL003 (LV_STL003_AR_Plate5)

description: Library name: LV_and_STL003_LV_STL003_AR_Plate5


title: C57_Spleen_KO_Male5

description:
Library name: C57_Spleen_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: C57_Spleen_KO_Male4

description:
Library name: C57_Spleen_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO1_n1_ns

description:
Library name: Sample 85
TO240_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: LV+STL003 (LV_STL003_AR_Plate4)

description: Library name: LV_and_STL003_LV_STL003_AR_Plate4


title: LV+STL003 (LV_STL003_AR_Plate3)

description: Library name: LV_and_STL003_LV_STL003_AR_Plate3


title: C57_Spleen_KO_Female3

description:
Library name: C57_Spleen_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Spleen


title: cDC1, Clec1a KO1_n1_necrocoli

description:
Library name: Sample 84
TO240_DGEseq.unq.refseq.umi.dat


title: LV+STL003 (LV_STL003_AR_Plate2)

description: Library name: LV_and_STL003_LV_STL003_AR_Plate2


title: C57_SpinalCord_WT_Male5

description:
Library name: C57_SpinalCord_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: SpinalCord

value: WT


title: C57_SpinalCord_WT_Male4

description:
Library name: C57_SpinalCord_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male


title: C57_SpinalCord_WT_Male3

description:
Library name: C57_SpinalCord_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO1_n1_ifn

description:
Library name: Sample 82
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: stimulated with type I IFN


title: C57_SpinalCord_WT_Male2

description:
Library name: C57_SpinalCord_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: LV+PT-1LGRB (LV_IOBHO_Tris_Plate4)

description: Library name: LV_and_PT-1LGRB_LV_IOBHO_Tris_Plate4

value: Left Ventricle


title: C57_SpinalCord_WT_Female3

description:
Library name: C57_SpinalCord_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female


title: cDC1, Clec1a KO1_n1_ecoli

description:
Library name: Sample 81
TO240_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: stimulated with E Coli


title: C57_SpinalCord_WT_Female2

description:
Library name: C57_SpinalCord_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7.5 months


title: LV+PT-1LGRB (LV_IOBHO_Tris_Plate3)

description: Library name: LV_and_PT-1LGRB_LV_IOBHO_Tris_Plate3


title: C57_SpinalCord_WT_Female1

description:
Library name: C57_SpinalCord_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: cDC1, Clec1a WT8_n4_ns

description:
Library name: Sample 80
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: Clec1a WT


title: C57_SpinalCord_KO_Male5

description:
Library name: C57_SpinalCord_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: LV+PT-1LGRB (LV_IOBHO_Tris_Plate2)

description: Library name: LV_and_PT-1LGRB_LV_IOBHO_Tris_Plate2


title: cDC1, Clec1a WT8_n4_necrocoli

description:
Library name: Sample 79
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells plus E Coli


title: C57_SpinalCord_KO_Male3

description:
Library name: C57_SpinalCord_KO_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: SpinalCord


title: C57_SpinalCord_KO_Male2

description:
Library name: C57_SpinalCord_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 9 weeks


title: cDC1, Clec1a WT8_n4_necro

description:
Library name: Sample 78
TO239_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: stimulated with necrotic cells


title: C57_SpinalCord_KO_Female3

description:
Library name: C57_SpinalCord_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: LV+PT-1LGRB (LV_IOBHO_Gly_Plate4)

description: Library name: LV_and_PT-1LGRB_LV_IOBHO_Gly_Plate4

value: Left Ventricle


title: C57_SpinalCord_KO_Female2

description:
Library name: C57_SpinalCord_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 8 months


title: LV+PT-1LGRB (LV_IOBHO_Tris_Plate1)

description: Library name: LV_and_PT-1LGRB_LV_IOBHO_Tris_Plate1


title: cDC1, Clec1a WT8_n4_ifn

description:
Library name: Sample 77
TO239_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: stimulated with type I IFN


title: C57_SpinalCord_KO_Female1

description:
Library name: C57_SpinalCord_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_SmallIntestine_WT_Male6

description:
Library name: C57_SmallIntestine_WT_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: SmallIntestine

value: SmallIntestine

value: WT


title: LV+PT-1LGRB (LV_IOBHO_Gly_Plate3)

description: Library name: LV_and_PT-1LGRB_LV_IOBHO_Gly_Plate3


title: cDC1, Clec1a WT8_n4_ecoli

description:
Library name: Sample 76
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with E Coli


title: LV+PT-1LGRB (LV_IOBHO_Gly_Plate2)

description: Library name: LV_and_PT-1LGRB_LV_IOBHO_Gly_Plate2


title: C57_SmallIntestine_WT_Male3

description:
Library name: C57_SmallIntestine_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: C57_SmallIntestine_WT_Male5

description:
Library name: C57_SmallIntestine_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT8_n3_ns

description:
Library name: Sample 75
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: Non stimulated


title: C57_SmallIntestine_WT_Male2

description:
Library name: C57_SmallIntestine_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 10 weeks


title: LV+PT-1LGRB (LV_IOBHO_Gly_Plate1)

description: Library name: LV_and_PT-1LGRB_LV_IOBHO_Gly_Plate1


title: C57_SmallIntestine_WT_Female3

description:
Library name: C57_SmallIntestine_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7.5 months


title: cDC1, Clec1a WT8_n3_necrocoli

description:
Library name: Sample 74
TO239_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: stimulated with necrotic cells plus E Coli


title: LG+PT-1LVAN (LG_JF1NZ_Plate9)

description: Library name: LG_and_PT-1LVAN_LG_JF1NZ_Plate9

source_name: Lung

value: Lung


title: C57_SmallIntestine_WT_Female2

description:
Library name: C57_SmallIntestine_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female


title: cDC1, Clec1a WT8_n3_necro

description:
Library name: Sample 73
TO239_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells


title: C57_SmallIntestine_WT_Female1

description:
Library name: C57_SmallIntestine_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: SmallIntestine


title: C57_SmallIntestine_KO_Male5

description:
Library name: C57_SmallIntestine_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: LG+PT-1LVAN (LG_JF1NZ_Plate8)

description: Library name: LG_and_PT-1LVAN_LG_JF1NZ_Plate8


title: C57_SmallIntestine_KO_Male4

description:
Library name: C57_SmallIntestine_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT8_n3_ifn

description:
Library name: Sample 72
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with type I IFN


title: LG+PT-1LVAN (LG_JF1NZ_Plate7)

description: Library name: LG_and_PT-1LVAN_LG_JF1NZ_Plate7


title: C57_SmallIntestine_KO_Female3

description:
Library name: C57_SmallIntestine_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_SmallIntestine_KO_Female2

description:
Library name: C57_SmallIntestine_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: cDC1, Clec1a WT8_n3_ecoli

description:
Library name: Sample 71
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: stimulated with E Coli


title: C57_SmallIntestine_KO_Female1

description:
Library name: C57_SmallIntestine_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: LG+PT-1LVAN (LG_JF1NZ_Plate6)

description: Library name: LG_and_PT-1LVAN_LG_JF1NZ_Plate6


title: C57_Prostate_WT_Male5

description:
Library name: C57_Prostate_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Prostate

value: Prostate

value: WT

value: Male

value: 8 weeks


title: C57_Prostate_WT_Male4

description:
Library name: C57_Prostate_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: LG+PT-1LVAN (LG_JF1NZ_Plate5)

description: Library name: LG_and_PT-1LVAN_LG_JF1NZ_Plate5

value: Lung


title: C57_Prostate_WT_Male3

description:
Library name: C57_Prostate_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT8_n2_necrocoli

description:
Library name: Sample 69
TO239_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells plus E Coli


title: C57_Prostate_WT_Male2

description:
Library name: C57_Prostate_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: LG+PT-1LVAN (LG_JF1NZ_Plate10)

description: Library name: LG_and_PT-1LVAN_LG_JF1NZ_Plate10


title: C57_Prostate_KO_Male5

description:
Library name: C57_Prostate_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: cDC1, Clec1a WT8_n2_necro

description:
Library name: Sample 68
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with necrotic cells


title: C57_Prostate_KO_Male4

description:
Library name: C57_Prostate_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_SpinalCord_KO_Male1

description:
Library name: C57_SpinalCord_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: SpinalCord


title: cDC1, Clec1a WT8_n2_ifn

description:
Library name: Sample 67
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: stimulated with type I IFN


title: C57_Prostate_KO_Male1

description:
Library name: C57_Prostate_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Prostate


title: C57_Prostate_KO_Male2

description:
Library name: C57_Prostate_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: C57_Pituitary_WT_Male5

description:
Library name: C57_Pituitary_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Pituitary

value: Pituitary

value: WT

value: Male


title: C57_Pituitary_WT_Male4

description:
Library name: C57_Pituitary_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: LG+PT-1JKYN (LG_ACCPU_Plate7)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate7

value: Lung


title: C57_Pituitary_WT_Male2

description:
Library name: C57_Pituitary_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: LG+PT-1JKYN (LG_ACCPU_Plate6)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate6


title: C57_Pituitary_WT_Male3

description:
Library name: C57_Pituitary_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_Pituitary_WT_Female3

description:
Library name: C57_Pituitary_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: cDC1, Clec1a WT8_n1_necrocoli

description:
Library name: Sample 64
TO239_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells plus E Coli


title: C57_Pituitary_WT_Female1

description:
Library name: C57_Pituitary_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: LG+PT-1JKYN (LG_ACCPU_Plate5)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate5


title: C57_Pituitary_KO_Male5

description:
Library name: C57_Pituitary_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: cDC1, Clec1a WT8_n1_necro

description:
Library name: Sample 63
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with necrotic cells


title: C57_Pituitary_KO_Male2

description:
Library name: C57_Pituitary_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: LG+PT-1JKYN (LG_ACCPU_Plate4)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate4


title: cDC1, Clec1a WT8_n1_ifn

description:
Library name: Sample 62
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: stimulated with type I IFN


title: C57_Pituitary_KO_Male1

description:
Library name: C57_Pituitary_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Pituitary


title: cDC1, Clec1a WT8_n2_ns

description:
Library name: Sample 70
TO239_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: C57_Pituitary_KO_Female2

description:
Library name: C57_Pituitary_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: LG+PT-1JKYN (LG_ACCPU_Plate3)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate3


title: C57_Pituitary_KO_Female1

description:
Library name: C57_Pituitary_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: cDC1, Clec1a WT8_n1_ecoli

description:
Library name: Sample 61
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: C57_Pancreas_WT_Male6

description:
Library name: C57_Pancreas_WT_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Pancreas

value: Pancreas

value: WT

value: Male


title: LG+PT-1JKYN (LG_ACCPU_Plate2)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate2

value: Lung


title: C57_Pancreas_WT_Male4

description:
Library name: C57_Pancreas_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: cDC1, Clec1a WT7_n4_ns

description:
Library name: Sample 60
TO239_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells


title: C57_Pancreas_WT_Male3

description:
Library name: C57_Pancreas_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: LG+PT-1JKYN (LG_ACCPU_Plate9)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate9


title: LG+PT-1JKYN (LG_ACCPU_Plate8)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate8


title: LG+PT-1JKYN (LG_ACCPU_Plate10)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate10


title: cDC1, Clec1a WT8_n2_ecoli

description:
Library name: Sample 66
TO239_DGEseq.unq.refseq.umi.dat

value: spleen


title: cDC1, Clec1a WT7_n4_necrocoli

description:
Library name: Sample 59
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with necrotic cells plus E Coli


title: C57_Pancreas_WT_Female3

description:
Library name: C57_Pancreas_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: C57_Pancreas_WT_Female1

description:
Library name: C57_Pancreas_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: LG+PT-1JKYN (LG_ACCPU_Plate1)

description: Library name: LG_and_PT-1JKYN_LG_ACCPU_Plate1


title: cDC1, Clec1a WT8_n1_ns

description:
Library name: Sample 65
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT


title: cDC1, Clec1a WT7_n4_necro

description:
Library name: Sample 58
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: C57_Pancreas_KO_Male6

description:
Library name: C57_Pancreas_KO_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: C57_Pancreas_KO_Male5

description:
Library name: C57_Pancreas_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: EG+PT-1LGRB (EG_IOBHM_AR_Plate8)

description: Library name: EG_and_PT-1LGRB_EG_IOBHM_AR_Plate8

source_name: Esophagus Muscularis Mucosa

value: Esophagus Muscularis Mucosa


title: cDC1, Clec1a KO1_n2_ns

description:
Library name: Sample 90
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: Non stimulated


title: C57_Pancreas_KO_Male4

description:
Library name: C57_Pancreas_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Pancreas

value: Male


title: C57_Spleen_WT_Male2

description:
Library name: C57_Spleen_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Spleen

value: WT

value: 10 weeks


title: EG+PT-1LGRB (EG_IOBHM_AR_Plate7)

description: Library name: EG_and_PT-1LGRB_EG_IOBHM_AR_Plate7


title: C57_Pancreas_KO_Female1

description:
Library name: C57_Pancreas_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: cDC1, Clec1a WT7_n4_ifn

description:
Library name: Sample 57
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with type I IFN


title: C57_Ovary_WT_Female3

description:
Library name: C57_Ovary_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Ovary

value: Ovary

value: Female

value: 7.5 months


title: cDC1, Clec1a WT7_n4_ecoli

description:
Library name: Sample 56
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: stimulated with E Coli


title: C57_Ovary_WT_Female2

description:
Library name: C57_Ovary_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: EG+PT-1LGRB (EG_IOBHM_AR_Plate6)

description: Library name: EG_and_PT-1LGRB_EG_IOBHM_AR_Plate6

value: Esophagus Muscularis Mucosa


title: cDC1, Clec1a WT7_n3_ns

description:
Library name: Sample 55
TO239_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: C57_Ovary_WT_Female1

description:
Library name: C57_Ovary_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: C57_Ovary_KO_Female3

description:
Library name: C57_Ovary_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: EG+PT-1LGRB (EG_IOBHM_AR_Plate5)

description: Library name: EG_and_PT-1LGRB_EG_IOBHM_AR_Plate5


title: C57_Spleen_KO_Male2

description:
Library name: C57_Spleen_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Spleen

value: Male


title: C57_Spleen_KO_Male1

description:
Library name: C57_Spleen_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: cDC1, Clec1a WT7_n3_necrocoli

description:
Library name: Sample 54
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells plus E Coli


title: C57_Ovary_KO_Female2

description:
Library name: C57_Ovary_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: EG+PT-1LGRB (EG_IOBHM_AR_Plate4)

description: Library name: EG_and_PT-1LGRB_EG_IOBHM_AR_Plate4


title: C57_Ovary_KO_Female1

description:
Library name: C57_Ovary_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: C57_Muscle_WT_Male6

description:
Library name: C57_Muscle_WT_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Muscle

value: Muscle

value: WT


title: C57_Spleen_KO_Female1

description:
Library name: C57_Spleen_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female


title: cDC1, Clec1a WT7_n3_necro

description:
Library name: Sample 53
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells


title: EG+PT-1LGRB (EG_IOBHM_AR_Plate3)

description: Library name: EG_and_PT-1LGRB_EG_IOBHM_AR_Plate3

value: Esophagus Muscularis Mucosa


title: C57_Muscle_WT_Male4

description:
Library name: C57_Muscle_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: LV+STL003 (LV_STL003_AR_Plate1)

description: Library name: LV_and_STL003_LV_STL003_AR_Plate1

value: Left Ventricle


title: cDC1, Clec1a KO1_n1_necro

description:
Library name: Sample 83
TO240_DGEseq.unq.refseq.umi.dat

value: Clec1a KO


title: C57_Muscle_WT_Male3

description:
Library name: C57_Muscle_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male


title: cDC1, Clec1a WT7_n3_ifn

description:
Library name: Sample 52
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: stimulated with type I IFN


title: C57_Muscle_WT_Male2

description:
Library name: C57_Muscle_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: EG+PT-1LGRB (EG_IOBHM_AR_Plate2)

description: Library name: EG_and_PT-1LGRB_EG_IOBHM_AR_Plate2


title: C57_Muscle_WT_Female3

description:
Library name: C57_Muscle_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7.5 months


title: C57_Muscle_KO_Male6

description:
Library name: C57_Muscle_KO_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: cDC1, Clec1a WT7_n3_ecoli

description:
Library name: Sample 51
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with E Coli


title: EG+PT-1LGRB (EG_IOBHM_AR_Plate1)

description: Library name: EG_and_PT-1LGRB_EG_IOBHM_AR_Plate1


title: cDC1, Clec1a WT7_n2_ns

description:
Library name: Sample 50
TO239_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: C57_Muscle_KO_Male4

description:
Library name: C57_Muscle_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Muscle


title: C57_Muscle_KO_Male5

description:
Library name: C57_Muscle_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: C57_Muscle_KO_Male3

description:
Library name: C57_Muscle_KO_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT7_n2_necrocoli

description:
Library name: Sample 49
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells plus E Coli


title: C57_Muscle_KO_Male1

description:
Library name: C57_Muscle_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: EG+PT-1JKYN (EG_A8CPH_AR_Plate8)

description: Library name: EG_and_PT-1JKYN_EG_A8CPH_AR_Plate8

value: Esophagus Muscularis Mucosa


title: C57_Muscle_KO_Female1

description:
Library name: C57_Muscle_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 9 weeks


title: cDC1, Clec1a WT7_n2_necro

description:
Library name: Sample 48
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: stimulated with necrotic cells


title: EG+PT-1JKYN (EG_A8CPH_AR_Plate7)

description: Library name: EG_and_PT-1JKYN_EG_A8CPH_AR_Plate7


title: EG+PT-1JKYN (EG_A8CPH_AR_Plate6)

description: Library name: EG_and_PT-1JKYN_EG_A8CPH_AR_Plate6


title: C57_Muscle_KO_Female2

description:
Library name: C57_Muscle_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: C57_LymphNode_WT_Male5

description:
Library name: C57_LymphNode_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: LymphNode

value: LymphNode

value: WT

value: Male

value: 8 weeks


title: EG+PT-1JKYN (EG_A8CPH_AR_Plate5)

description: Library name: EG_and_PT-1JKYN_EG_A8CPH_AR_Plate5


title: C57_LymphNode_WT_Male4

description:
Library name: C57_LymphNode_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_LymphNode_WT_Male3

description:
Library name: C57_LymphNode_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT7_n2_ifn

description:
Library name: Sample 47
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with type I IFN


title: cDC1, Clec1a WT7_n2_ecoli

description:
Library name: Sample 46
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: C57_LymphNode_WT_Male2

description:
Library name: C57_LymphNode_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: C57_LymphNode_WT_Female3

description:
Library name: C57_LymphNode_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7.5 months


title: EG+PT-1JKYN (EG_A8CPH_AR_Plate4)

description: Library name: EG_and_PT-1JKYN_EG_A8CPH_AR_Plate4


title: cDC1, Clec1a WT7_n1_ns

description:
Library name: Sample 45
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Non stimulated


title: EG+PT-1JKYN (EG_A8CPH_AR_Plate3)

description: Library name: EG_and_PT-1JKYN_EG_A8CPH_AR_Plate3

value: Esophagus Muscularis Mucosa


title: C57_LymphNode_WT_Female2

description:
Library name: C57_LymphNode_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female


title: C57_LymphNode_WT_Female1

description:
Library name: C57_LymphNode_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT7_n1_necrocoli

description:
Library name: Sample 44
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: stimulated with necrotic cells plus E Coli


title: EG+PT-1JKYN (EG_A8CPH_AR_Plate2)

description: Library name: EG_and_PT-1JKYN_EG_A8CPH_AR_Plate2


title: C57_LymphNode_KO_Male6

description:
Library name: C57_LymphNode_KO_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: LymphNode

value: Mecp2 KO


title: C57_LymphNode_KO_Male5

description:
Library name: C57_LymphNode_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 7 weeks


title: cDC1, Clec1a WT7_n1_necro

description:
Library name: Sample 43
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells


title: EG+PT-1JKYN (EG_A8CPH_AR_Plate1)

description: Library name: EG_and_PT-1JKYN_EG_A8CPH_AR_Plate1


title: C57_LymphNode_KO_Male4

description:
Library name: C57_LymphNode_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: C57_LymphNode_KO_Female3

description:
Library name: C57_LymphNode_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a WT7_n1_ifn

description:
Library name: Sample 42
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with type I IFN


title: C57_LymphNode_KO_Female2

description:
Library name: C57_LymphNode_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: B+PT-1LVAN (B_JF1NV_Plate2)

description: Library name: B_and_PT-1LVAN_B_JF1NV_Plate2

source_name: Breast

value: Breast


title: C57_Lung_WT_Male5

description:
Library name: C57_Lung_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Lung

value: WT


title: C57_Lung_WT_Male4

description:
Library name: C57_Lung_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: B+PT-1LVAN (B_JF1NV_Plate1)

description: Library name: B_and_PT-1LVAN_B_JF1NV_Plate1


title: cDC1, Clec1a WT7_n1_ecoli

description:
Library name: Sample 41
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with E Coli


title: B+PT-1LVAN (B_JF1NV_AR_Plate4)

description: Library name: B_and_PT-1LVAN_B_JF1NV_AR_Plate4


title: C57_Lung_WT_Male2

description:
Library name: C57_Lung_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: cDC1, Clec1a WT5_n4_ifn

description:
Library name: Sample 217
TO241_DGEseq.unq.refseq.umi.dat

value: Clec1a WT


title: cDC1, Clec1a WT5_n4_ns

description:
Library name: Sample 220
TO241_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: cDC1, Clec1a KO8_n4_necrocoli

description:
Library name: Sample 39
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: stimulated with necrotic cells plus E Coli


title: C57_Lung_WT_Male3

description:
Library name: C57_Lung_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male


title: C57_Lung_WT_Female3

description:
Library name: C57_Lung_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: cDC1, Clec1a WT5_n4_necrocoli

description:
Library name: Sample 219
TO241_DGEseq.unq.refseq.umi.dat

value: spleen


title: cDC1, Clec1a KO8_n4_ns

description:
Library name: Sample 40
TO239_DGEseq.unq.refseq.umi.dat


title: C57_Lung_WT_Female2

description:
Library name: C57_Lung_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO8_n4_necro

description:
Library name: Sample 38
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: B+PT-1LVAN (B_JF1NV_AR_Plate3)

description: Library name: B_and_PT-1LVAN_B_JF1NV_AR_Plate3

value: Breast


title: C57_Lung_WT_Female1

description:
Library name: C57_Lung_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Lung

value: 8 weeks


title: B+PT-1LVAN (B_JF1NV_AR_Plate2)

description: Library name: B_and_PT-1LVAN_B_JF1NV_AR_Plate2


title: C57_Lung_KO_Male5

description:
Library name: C57_Lung_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: cDC1, Clec1a KO8_n4_ifn

description:
Library name: Sample 37
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with type I IFN


title: C57_Lung_KO_Male4

description:
Library name: C57_Lung_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: B+PT-1LVAN (B_JF1NV_AR_Plate1)

description: Library name: B_and_PT-1LVAN_B_JF1NV_AR_Plate1


title: C57_Lung_KO_Male2

description:
Library name: C57_Lung_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: cDC1, Clec1a KO8_n4_ecoli

description:
Library name: Sample 36
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: stimulated with E Coli


title: C57_Lung_KO_Male1

description:
Library name: C57_Lung_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male


title: Gene expression profiles of liver of four choline-deficient diet rats at 7 weeks of age, sample 2

type: RNA

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

organism: Rattus norvegicus

source_name: CDD

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: Rats were maintained in accordance with the Hiroshima University guidelines for the care and use of laboratory animals.

extract_protocol: Total RNAs of liver were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: 7 weeks old Wister rats were fed either a choline-deficient diet or control diet for 10 days

value: liver

value: choline-deficient diet

source_name: cont

value: control


title: B+PT-1LGRB (B_IOBHL_Plate9)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate9


title: Gene expression profiles of liver of four choline-deficient diet rats at 7 weeks of age, sample 1


title: cDC1, Clec1a KO8_n3_ns

description:
Library name: Sample 35
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: Non stimulated


title: B+PT-1LGRB (B_IOBHL_Plate7)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate7

value: Breast


title: Tam_24h_4

city: Mishima

first: Hajime

last: Okada

state: Shizuoka

address: Yata 1111

institute: National Institute of Genetics

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequeced reads were mapped to mm10 genome with Hisat2 as the aligner.
The abundance of each transcript model and statistical results were computed using DEseq2 based on UCSC genome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file was generated using DEseq2

source_name: established cell line from adult biliary ducts

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen).
Libraries were prepared from 600 to 1100 ng of total RNA with the TruSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions.

tag: agent

value: 4-OH Tamoxifen


title: cDC1, Clec1a KO8_n3_necrocoli

description:
Library name: Sample 34
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells plus E Coli


title: C57_Lung_KO_Female3

description:
Library name: C57_Lung_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Lung

value: Mecp2 KO

value: Female

value: 7.5 months


title: Tam_24h_3


title: C57_Lung_KO_Female2

description:
Library name: C57_Lung_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: B+PT-1LGRB (B_IOBHL_Plate8)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate8


title: Tam_24h_2


title: cDC1, Clec1a KO8_n3_necro

description:
Library name: Sample 33
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells


title: B+PT-1LGRB (B_IOBHL_Plate6)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate6


title: cDC1, Clec1a KO8_n3_ifn

description:
Library name: Sample 32
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: stimulated with type I IFN


title: B+PT-1LGRB (B_IOBHL_Plate5)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate5


title: Tam_24h_1


title: B+PT-1LGRB (B_IOBHL_Plate3)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate3


title: cDC1, Clec1a KO8_n2_necrocoli

description:
Library name: Sample 29
TO239_DGEseq.unq.refseq.umi.dat


title: Control_24h_3

value: EtOH control


title: cDC1, Clec1a KO8_n3_ecoli

description:
Library name: Sample 31
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with E Coli


title: C57_Liver_WT_Male4

description:
Library name: C57_Liver_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Liver

value: Liver

value: WT

value: Male

value: 8 weeks


title: B+PT-1LGRB (B_IOBHL_Plate2)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate2

value: Breast


title: cDC1, Clec1a KO8_n2_necro

description:
Library name: Sample 28
TO239_DGEseq.unq.refseq.umi.dat

source_name: spleen


title: C57_Liver_WT_Male2

description:
Library name: C57_Liver_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: Control_24h_1


title: Tam_12h_4

value: 4-OH Tamoxifen


title: C57_LymphNode_KO_Female1

description:
Library name: C57_LymphNode_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: LymphNode

value: Mecp2 KO

value: Female

value: 9 weeks


title: cDC1, Clec1a KO8_n2_ecoli

description:
Library name: Sample 26
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells


title: Tam_12h_3


title: cDC1, Clec1a KO8_n1_ns

description:
Library name: Sample 25
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: Non stimulated


title: C57_Liver_WT_Female1

description:
Library name: C57_Liver_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: Tam_12h_2


title: C57_Liver_KO_Male5

description:
Library name: C57_Liver_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: AG+STL003 (AG_STL003_AR_Plate4)

description: Library name: AG_and_STL003_AG_STL003_AR_Plate4

source_name: Adrenal Gland

value: Adrenal Gland


title: cDC1, Clec1a KO8_n1_necro

description:
Library name: Sample 23
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells


title: AG+STL003 (AG_STL003_AR_Plate3)

description: Library name: AG_and_STL003_AG_STL003_AR_Plate3


title: Control_12h_4

value: EtOH control


title: C57_Lung_KO_Female1

description:
Library name: C57_Lung_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Lung


title: AG+STL003 (AG_STL003_AR_Plate2)

description: Library name: AG_and_STL003_AG_STL003_AR_Plate2


title: C57_Liver_KO_Male1

description:
Library name: C57_Liver_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Liver

value: Male


title: Control_24h_4


title: C57_Liver_WT_Male5

description:
Library name: C57_Liver_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WT

value: 8 weeks


title: B+PT-1LGRB (B_IOBHL_Plate4)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate4

value: Breast


title: cDC1, Clec1a KO8_n2_ns

description:
Library name: Sample 30
TO239_DGEseq.unq.refseq.umi.dat


title: C57_Liver_WT_Male3

description:
Library name: C57_Liver_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: Control_24h_2


title: cDC1, Clec1a KO8_n1_ecoli

description:
Library name: Sample 21
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: Control_12h_3


title: C57_Liver_KO_Female3

description:
Library name: C57_Liver_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: Female

value: 7.5 months


title: B+PT-1LGRB (B_IOBHL_Plate10)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate10


title: cDC1, Clec1a KO8_n2_ifn

description:
Library name: Sample 27
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Clec1a KO

value: stimulated with type I IFN


title: AG+STL003 (AG_STL003_AR_Plate1)

description: Library name: AG_and_STL003_AG_STL003_AR_Plate1

value: Adrenal Gland


title: cDC1, Clec1a KO7_n4_ns

description:
Library name: Sample 20
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: Non stimulated


title: Control_12h_1

value: EtOH control


title: C57_Liver_WT_Female3

description:
Library name: C57_Liver_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Liver


title: B+PT-1LGRB (B_IOBHL_Plate1)

description: Library name: B_and_PT-1LGRB_B_IOBHL_Plate1


title: C57_Liver_KO_Female2

description:
Library name: C57_Liver_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate9)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate9


title: C57_Liver_WT_Female2

description:
Library name: C57_Liver_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WT


title: AG+STL003 (AG_STL003_AR_Plate6)

description: Library name: AG_and_STL003_AG_STL003_AR_Plate6


title: C57_Liver_KO_Female1

description:
Library name: C57_Liver_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: cDC1, Clec1a KO7_n4_necrocoli

description:
Library name: Sample 19
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells plus E Coli


title: ACHN cells, SMAL-329 8 uM, 24 hours Replicate 3

city: San Francisco

first: John

last: Gordan

address: 1700 4th Street

institute: UC San Francisco

description: Library name: ACHN_SU329_8uM_R3

data_processing:
Kallisto and DESeq2
Assembly: hg38

source_name: cell line

growth_protocol: Eagles MEM with full additives

extract_protocol:
Qiagen RNEasy
NEBNext Ultra™ II DNA Library Prep Kit

treatment_protocol: 24 hours of 8 uM SMALS-329 or vehicle

value: cell line

tag: cell line

value: ACHN

value: renal papillary carcinoma


title: ACHN cells, SMAL-329 8 uM, 24 hours Replicate 2

description: Library name: ACHN_SU329_8uM_R2


title: cDC1, Clec1a KO7_n4_necro

description:
Library name: Sample 18
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with necrotic cells


title: C57_LargeIntestine_WT_Male5

description:
Library name: C57_LargeIntestine_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: LargeIntestine

value: LargeIntestine

value: Male

value: 8 weeks


title: ACHN cells, SMAL-329 8 uM, 24 hours Replicate 1

description: Library name: ACHN_SU329_8uM_R1


title: AG+STL003 (AG_STL003_AR_Plate5)

description: Library name: AG_and_STL003_AG_STL003_AR_Plate5

value: Adrenal Gland


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate7)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate7


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate8)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate8


title: cDC1, Clec1a KO7_n4_ifn

description:
Library name: Sample 17
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Clec1a KO

value: stimulated with type I IFN


title: C57_LargeIntestine_WT_Male4

description:
Library name: C57_LargeIntestine_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WT


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate6)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate6


title: ACHN cells, DMSO, 24 hours Replicate 3

description: Library name: ACHN_DMSO_R3


title: cDC1, Clec1a KO8_n1_necrocoli

description:
Library name: Sample 24
TO239_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a KO7_n4_ecoli

description:
Library name: Sample 16
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate5)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate5


title: C57_LargeIntestine_WT_Male3

description:
Library name: C57_LargeIntestine_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: ACHN cells, DMSO, 24 hours Replicate 2

description: Library name: ACHN_DMSO_R2


title: cDC1, Clec1a KO7_n3_ns

description:
Library name: Sample 15
TO239_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: Tam_12h_1

value: 4-OH Tamoxifen


title: C57_LargeIntestine_WT_Male2

description:
Library name: C57_LargeIntestine_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate4)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate4


title: ACHN cells, DMSO, 24 hours Replicate 1

description: Library name: ACHN_DMSO_R1

value: cell line

value: ACHN

value: renal papillary carcinoma


title: cDC1, Clec1a KO7_n3_necrocoli

description:
Library name: Sample 14
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with necrotic cells plus E Coli


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate3)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate3


title: C57_LargeIntestine_WT_Female3

description:
Library name: C57_LargeIntestine_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: LargeIntestine

value: Female

value: 7.5 months


title: cDC1, Clec1a KO7_n3_necro

description:
Library name: Sample 13
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: 8-12 weeks old

value: stimulated with necrotic cells


title: 19_022H1_Adrenal

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description:
Library name: 19_022H1_Adrenal
19_022H1_Adrenal

data_processing:
The sequencing reads were analyzed with human reference genome GRCh38 using Cell Ranger v7.1.0 [1]. Introns were included in the analysis
raw bcl files were processed using cellranger mkfastq and cellranger count
Assembly: hg38
Supplementary files format and content: barcodes.tsv, genes.tsv and matrix.mtx ( 3 files per sample, output from cellranger count) are submitted as processed files. Additionally "possorted_genome_bam.bam" are submitted as raw files per sample.

extract_protocol:
We isolated nuclei from OCT-embedded frozen human bladder cancer tissue samples and constructed 3’ single-cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system
RNA libraries were prepared for sequencing using Single Cell Library Kit from 10x Genomics (P/N 120218) according to manufacturer's guidelines.


title: C57_LargeIntestine_WT_Female2

description:
Library name: C57_LargeIntestine_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate2)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate2

value: Adrenal Gland


title: 19_022I1_Liver

description:
Library name: 19_022I1_Liver
19_022I1_Liver


title: C57_Liver_KO_Male4

description:
Library name: C57_Liver_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Liver

value: Mecp2 KO

value: Male

value: 8 weeks


title: cDC1, Clec1a KO7_n3_ifn

description:
Library name: Sample 12
TO239_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: Clec1a KO

value: stimulated with type I IFN


title: C57_LargeIntestine_WT_Female1

description:
Library name: C57_LargeIntestine_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WT


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate10)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate10


title: 18_120L1_LN

description:
Library name: 18_120L1_LN
18_120L1_LN


title: cDC1, Clec1a KO7_n3_ecoli

description:
Library name: Sample 11
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with E Coli


title: C57_LargeIntestine_KO_Male6

description:
Library name: C57_LargeIntestine_KO_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: LargeIntestine


title: AG+PT-1K2DA (AG_JF1NQ_AR_Plate1)

description: Library name: AG_and_PT-1K2DA_AG_JF1NQ_AR_Plate1


title: cDC1, Clec1a KO7_n2_ns

description:
Library name: Sample 10
TO239_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: 17_071I1_Omentum

description:
Library name: 17_071I1_Omentum
17_071I1_Omentum


title: 16_079P4_Bladder

description:
Library name: 16_079P4_Bladder
16_079P4_Bladder


title: PT9,MetastasisTumor2,vdj_t

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

description:
Library name: PT9.S13.MetastasisTumor2.Mixed.vdj_t
10x Genomics

data_processing:
For scRNA-seq, raw reads were demultiplexed with Cell Ranger (v6.0.0 or v7.1.0) and mapped to the human genome (GRCh38). Ambient RNA was removed using SoupX, and doublets were filtered with scDblFinder. Quality control in Seurat excluded cells with <200 or >7,500 unique features, <400 or >40,000 total RNA counts, or >10% mitochondrial content. For V(D)J sequencing, the djvdj (v0.1.0) package was utilized, retaining only cells with high-quality transcriptomic data. Samples with fewer than 10 cells were excluded for robustness. Clonotypes were defined by CDR3 amino acid sequences, and only those with exactly two chains were retained; cells without an assigned clonotype were removed. For Visium HD, images were aligned in Loupe Browser (v8.0.0), and Space Ranger (v3.1.0) was used for mapping. Bin2cell (v0.3.3) aggregated 2 μm bins to reconstruct single-cell-like profiles based on H&E morphology and gene expression at 0.5 μm per pixel resolution. Downstream analysis was performed in Scanpy, excluding cells with <100 or >40,000 features or >20% mitochondrial content.
Assembly: HG38
Supplementary files format and content: HDF5, csv and tsv of processed data
Library strategy: TCR-Seq

source_name: Thymus

extract_protocol:
Fresh thymus samples were obtained for scRNA-seq plus V(D)J sequencing and formalin-fixed, paraffin-embedded specimens were used for Visium HD spatial transcriptomics.
For scRNA-seq (3' v3) and scRNA-seq with V(D)J sequencing (5'), libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3 or Single Cell 5' Expression Assay and sequenced on NextSeq 1000/2000 or Illumina NovaSeq 6000 instruments. For Visium HD, samples were sectioned at 5 μm and processed at the Northwestern University NUSeq Core following the manufacturer’s protocol (Visium HD v1). These libraries were subsequently sequenced on an Illumina NovaSeq X Plus.

value: T cells

value: Thymus


title: C57_LargeIntestine_KO_Male5

description:
Library name: C57_LargeIntestine_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: cDC1, Clec1a KO8_n1_ifn

description:
Library name: Sample 22
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: 8-12 weeks old


title: C57_LargeIntestine_KO_Male4

description:
Library name: C57_LargeIntestine_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: 16_079N3_LN

description:
Library name: 16_079N3_LN
16_079N3_LN


title: PT9,Thymoma_MG,vdj_t

description:
Library name: PT9.S12.Thymoma_MG.Mixed.vdj_t
10x Genomics


title: PT9,MetastasisTumor1,vdj_t

description:
Library name: PT9.S11.MetastasisTumor1.Mixed.vdj_t
10x Genomics


title: 16_079H1_Liver

description:
Library name: 16_079H1_Liver
16_079H1_Liver


title: cDC1, Clec1a KO7_n2_ifn

description:
Library name: Sample 7
TO239_DGEseq.unq.refseq.umi.dat


title: C57_LargeIntestine_KO_Female3

description:
Library name: C57_LargeIntestine_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: 15_109G5_Liver

description:
Library name: 15_109G5_Liver
15_109G5_Liver


title: C57_LargeIntestine_KO_Female2

description:
Library name: C57_LargeIntestine_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 8 months


title: cDC1, Clec1a KO7_n2_ecoli

description:
Library name: Sample 6
TO239_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells


title: PT9,Thymus_MG,vdj_t

description:
Library name: PT9.S10.Thymus_MG.Mixed.vdj_t
10x Genomics


title: PT8,Thymus_no_MG,vdj_t

description:
Library name: PT8.S9.Thymus_no_MG.Mixed.vdj_t
10x Genomics


title: 19_007D5_Bladder

description:
Library name: 19_007D5_Bladder
19_007D5_Bladder


title: cDC1, Clec1a KO7_n1_ns

description:
Library name: Sample 5
TO239_DGEseq.unq.refseq.umi.dat

value: Clec1a KO


title: C57_LargeIntestine_KO_Female1

description:
Library name: C57_LargeIntestine_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: cDC1, Clec1a KO7_n1_necrocoli

description:
Library name: Sample 4
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells plus E Coli


title: 19_007K3_LN

description:
Library name: 19_007K3_LN
19_007K3_LN


title: PT7,Thymus_MG,vdj_t

description:
Library name: PT7.S8.Thymus_MG.Mixed.vdj_t
10x Genomics


title: PT6,Thymus_MG,vdj_t

description:
Library name: PT6.S7.Thymus_MG.Mixed.vdj_t
10x Genomics


title: C57_Kidney_WT_Male5

description:
Library name: C57_Kidney_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Kidney

value: Kidney

value: WT

value: Male

value: 8 weeks


title: 17_026K2_Bladder

description:
Library name: 17_026K2_Bladder
17_026K2_Bladder


title: cDC1, Clec1a KO7_n1_necro

description:
Library name: Sample 3
TO239_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with necrotic cells


title: C57_Kidney_WT_Male4

description:
Library name: C57_Kidney_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: cDC1, Clec1a KO7_n1_ifn

description:
Library name: Sample 2
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with type I IFN


title: 17_026J3_Omentum

description:
Library name: 17_026J3_Omentum
17_026J3_Omentum


title: C57_Kidney_WT_Male3

description:
Library name: C57_Kidney_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: PT5,Thymus_MG,vdj_t

description:
Library name: PT5.S6.Thymus_MG.Mixed.vdj_t
10x Genomics

value: T cells

value: Thymus


title: cDC1, Clec1a KO7_n2_necrocoli

description:
Library name: Sample 9
TO239_DGEseq.unq.refseq.umi.dat

value: spleen

value: 8-12 weeks old


title: 17_030G1_Liver

description:
Library name: 17_030G1_Liver
17_030G1_Liver


title: cDC1, Clec1a KO7_n1_ecoli

description:
Library name: Sample 1
TO239_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli