title: Neo_iCM, MGT+GW501516 replicate 2, Day14

description: Library name: MGT_GW501516_2


title: Neural precursor cell 763-1 ZIKV infection 12 hours post infection replicate 3

status: Public on Apr 23 2025

type: SRA

city: Southampton

first: Rob

last: Ewing

state: Hampshire

address: University Rd, Southampton

department: School of Biological Sciences

country: United Kingdom

institute: University of Southampton

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N3_Z12_3

library_source: transcriptomic

data_processing:
Assembly: HISAT2
quality control checks on raw sequence data  was performed usingFastQC (V0.11.9-0)
Sequence reads were trimmed for low quality sequences and adapters using Trim galore (version 0.6.6-0)
Reads were aligned against the Homo Sapien GRCh38 and ZIKV BeH819966 genome using HISAT2 (V2.2.0)
Read counts were obtained using FeatureCounts via the Subread package (Version 2.0.6)
Supplementary files format and content: Tab-dellmited text files with raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Cerebellum

growth_protocol: monolayer under standard conditions (5% CO2, 37°C)

extract_protocol:
High-quality total RNA was purified using the Monarch Total RNA Miniprep Kit (NEB #T2010S) as per the manufacturer’s protocol
mRNA library preparation (poly A enrichment)

treatment_protocol: Infected at multiplicity of infection (MOI) of 2 for 60 minutes

tag: tissue

value: Cerebellum

tag: cell line

tag: cell type

value: hiPSC-derived NPC from CZS-affected twin

tag: genotype

value: WT

tag: treatment

value: Infection with ZIKV (Strain KU365779.1) for 12 hours


title: H460 siCtrl 8gy ATAC-seq A

city: Morgantown

first: Emily

last: Westemeier-Rice

state: WV

address: 1 Medical Center Drive

country: USA

institute: West Virginia University

library_source: genomic

data_processing:
Reads were processed by WVU's Bioinformatics Core
Trimming (Bowtie2), alignment (SubRead) and filtering, Peak calling and visualization (featureCounts)
Assembly: hg38
Supplementary files format and content: NarrowPeak Files containing peak locations, summit, p-value and q-value

molecule: genomic DNA

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, and antibiotics in a humidified atmosphere at 5% CO2

extract_protocol:
DNA was .
After irradiation, 50,000 cells were removed for ATAC-Seq library preparation, the rest for further analysis to ensure effective knockdown of lnc-RAINY. The ATAC-Seq library was prepared as follows. Cells were centrifuged at 500xg at 4C for 5 min and supernatant was removed. Pellet was resuspended in RSB Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 1uL/mL each of Digitonin, Tween 20 and NP40) and incubated on ice 3 min. RSB-without (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 1uL/mL Tween 20) was added and the cells were centrifuged at 500xg for 10 min. Cells were resuspended in Transposition Mix (2x TD buffer 2.5uL transposase (Illumina cat#20043196), 1uL/100uL each of Digitonin and Tween 20, water and PBS). Tubes were then incubated at 37C shaking at 1000rpm for 30 min. Reaction was cleaned using Qiagen PCR Purification Kit with 3M sodium acetate. Sample was eluted in an elution buffer and prepped for PCR Amplification. Barcoded Primers were added to each sample with 2x NEBNext Master mix (NEB cat#M0541S). Samples were PCR amplified for 12 cycles and purified using Qiagen PCR Purification Kit, eluted in water. Samples were loaded on a 2% agarose e-gel and ran 3 minutes. Each lane was cut from the gel and the DNA extracted via Qiagen gel Purification kit.

treatment_protocol: Cells were treated with 300 pmol siRNA scramble or 100pmol each of 3 siRNAs designed against lnc-RAINY (designated siPool), 24 hours later, cells were treated with 8gy radiation, then left to recover for 72 hours before RNA extraction

value: NSCLC Male Lung Epithelial

tag: sample group

value: siCtrl 8gy


title: Neo_iCM, MGT+GW501516 replicate 1, Day14

city: wuhan

first: yu

middle: zhang

last: yi

state: hubei

address: donghu street

department: wuhan

country: China

institute: wuhan university

description: Library name: MGT_GW501516_1

data_processing:
Raw sequencing data was initially filtered by Trimmomatic (version 0.36), with the discarding of low-quality reads and the trimming of reads contaminated with adaptor sequences.
Clean reads were mapped to the reference genome of mouse (mm10) using hisat2 software with default parameters.
The counting of reads mapped to the exon regions of each gene was carried out by featureCounts (Subread-1.5.1; Bioconductor).
Resulting BAM files were sorted and indexed using SAMtools.
Assembly: mm10
Supplementary files format and content: raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: heart

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, cat. NO15596026). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: Primary cell

value: cardiac fibroblast

tag: age


title: H460 siCtrl NR ATAC-seq A

value: siCtrl NR


title: Neural precursor cell 763-1 ZIKV infection 12 hours post infection replicate 1

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N3_Z12_1


title: Neo_iCM, MGT+ZLN005 replicate 2, Day14

description: Library name: MGT_ZLN005_2


title: Neo_iCM, MGT+ZLN005 replicate 1, Day14

description: Library name: MGT_ZLN005_1


title: 14H133 [re-analysis]

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: reanalysis of GSM2834497

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters for samples sequenced using stranded libraries.
Strand orientation is reverse for stranded samples, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

source_name: Blood

extract_protocol:
KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Sequencing libraries were prepared from total RNA using a poly-A selection and either the TruSeq unstranded RNA Sample Preparation (Illumina), TruSeq Stranded RNA Sample Preparation (Illumina) or the KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

value: Blood

value: acute promyelocytic leukemia

tag: strand orientation

value: reverse


title: 14H071 [re-analysis]

description: reanalysis of GSM2834496

source_name: Bone marrow

value: Bone marrow


title: DAOY uninfected replicate 3

description:
Medulloblastoma cell line (DAOY) uninfected control
DY_ZC_3

value: DAOY

value: Medulloblastoma


title: 14H018 [re-analysis]

description: reanalysis of GSM2834495


title: Neo_iCM, MGT+DMSO replicate 1, Day14

description: Library name: MGT_DMSO_1

value: MGT+DMSO


title: 13H162 [re-analysis]

description: reanalysis of GSM2834494


title: 13H071 [re-analysis]

description: reanalysis of GSM2834492


title: 13H126 [re-analysis]

description: reanalysis of GSM2834493


title: H460 siCtrl 8gy ATAC-seq B


title: 11H043 [re-analysis]

description: reanalysis of GSM2834491


title: 10H110 [re-analysis]

description: reanalysis of GSM2834490


title: Neo_iCM, MGT+DMSO replicate 2, Day14

description: Library name: MGT_DMSO_2


title: DAOY uninfected replicate 1

description:
Medulloblastoma cell line (DAOY) uninfected control
DY_ZC_1

value: Cerebellum


title: 10H059 [re-analysis]

description: reanalysis of GSM2834489


title: Neo_CF, replicate 2, Day14

description: Library name: NeoCF_2

value: NeoCF


title: DAOY ZIKV infection 24 hours post infection replicate 3

description:
Medulloblastoma cell line (DAOY) infected for 24 hours with ZIKV (Strain KU365779.1)
DY_Z24_3

value: WT

value: Infection with ZIKV (Strain KU365779.1) for 24 hours


title: H460 siPool NR ATAC-seq A

value: NSCLC Male Lung Epithelial

value: siPool NR


title: 10H017 [re-analysis]

description: reanalysis of GSM2834487


title: Neural precursor cell 763-1 ZIKV infection 12 hours post infection replicate 2

description:
Induced pluripotent stem cell (hiPSC) derived neural precursor cell (NPC) infected for 12 hours with ZIKV (Strain KU365779.1)
N3_Z12_2

value: hiPSC-derived NPC from CZS-affected twin

value: Infection with ZIKV (Strain KU365779.1) for 12 hours


title: DAOY uninfected replicate 2

description:
Medulloblastoma cell line (DAOY) uninfected control
DY_ZC_2


title: POU2F2 OE P14 CD8+ T cells, Day14 post infection

city: Beijing

first: Min

last: Peng

address: Haidian

institute: Tsinghua university

description: Library name: CG

library_source: transcriptomic single cell

data_processing:
Downstream analyses were performed in R using the Seurat package. Cells in which fewer than 500 genes or more than 3000 genes were detected and in which mitochondrially encoded transcripts constituted greater than 5% of the total library were excluded from downstream analysis. Before following analysis, cells which were not αβT cells were identified by scaled expression of marker genes > 0.5 (δγT cell: Trgv2 and Tcrg-C2. Antigen presenting cells: Cd74. Machrophage: S100a8 and Lyz2, Treg: Foxp3) and excluded, yielding an expression matrix of 13588 cells by 19875 genes (Over-expression experiments, including Empty and Pou2f2). Each gene expression measurement was normalized by total expression in the corresponding cell and multiplied by a scaling factor of 10,000. Top 2000 variable genes were identified by FindVariableFeatures and used to execute PCA by RunPCA function of Seurat. Principal components were determined to be significant (P < 0.01) using the jackstraw method, and UMAP and clustering was performed on these significant principal components. Differential expression analysis was performed between each cluster and all other cells using a Wilcoxon rank sum test.
Assembly: mm10
Supplementary files format and content: tar files include barcodes, genes and matrix for each sample

source_name: spleen

extract_protocol:
Single-cell suspensions (2×105 cells/mL) with PBS were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron).

value: spleen

value: P14 CD8+ T cell

value: T cell


title: DAOY ZIKV infection 24 hours post infection replicate 2

description:
Medulloblastoma cell line (DAOY) infected for 24 hours with ZIKV (Strain KU365779.1)
DY_Z24_2


title: 09H073 [re-analysis]

description: reanalysis of GSM2834486

value: acute promyelocytic leukemia


title: 09H035 [re-analysis]

description: reanalysis of GSM2834484

value: reverse


title: DAOY ZIKV infection 24 hours post infection replicate 1

description:
Medulloblastoma cell line (DAOY) infected for 24 hours with ZIKV (Strain KU365779.1)
DY_Z24_1


title: 09H053 [re-analysis]

description: reanalysis of GSM2834485

value: Blood


title: 07H052 [re-analysis]

description: reanalysis of GSM2834483

value: Bone marrow


title: 10H023 [re-analysis]

description: reanalysis of GSM2834488


title: Empty OE P14 CD8+ T cells, Day14 post infection

description: Library name: CP


title: DAOY ZIKV infection 18 hours post infection replicate 3

description:
Medulloblastoma cell line (DAOY) infected for 18 hours with ZIKV (Strain KU365779.1)
DY_Z18_3

value: DAOY

value: Medulloblastoma

value: Infection with ZIKV (Strain KU365779.1) for 18 hours


title: Neo_CF, replicate 1, Day14

description: Library name: NeoCF_1

value: heart

value: Primary cell

value: cardiac fibroblast

value: NeoCF


title: DAOY ZIKV infection 18 hours post infection replicate 2

description:
Medulloblastoma cell line (DAOY) infected for 18 hours with ZIKV (Strain KU365779.1)
DY_Z18_2

value: Cerebellum

value: WT


title: P14 CD8+ T cells sgBcor/Zc3h12a, Day14

description: Library name: S34

data_processing:
Downstream analyses were performed in R using the Seurat package. Cells in which fewer than 500 genes or more than 3000 genes were detected and in which mitochondrially encoded transcripts constituted greater than 5% of the total library were excluded from downstream analysis. Before following analysis, cells which were not αβT cells were identified by scaled expression of marker genes > 0.5 (δγT cell: Trgv2 and Tcrg-C2. Antigen presenting cells: Cd74. Machrophage: S100a8 and Lyz2, Treg: Foxp3) and excluded, yielding an expression matrix of 13588 cells by 19875 genes (Over-expression experiments, including Empty and Pou2f2), and 39026 cells by 19804 genes (Knock out experiments, including sgControl, sgBcor, sgZc3h12a, sgBcor/Zc3h12a). Each gene expression measurement was normalized by total expression in the corresponding cell and multiplied by a scaling factor of 10,000. Top 2000 variable genes were identified by FindVariableFeatures and used to execute PCA by RunPCA function of Seurat. Principal components were determined to be significant (P < 0.01) using the jackstraw method, and UMAP and clustering was performed on these significant principal components. Differential expression analysis was performed between each cluster and all other cells using a Wilcoxon rank sum test.
Assembly: mm10
Supplementary files format and content: tar files include barcodes, genes and matrix for each sample


title: 14H038 [re-analysis]

description: reanalysis of GSM1636929

extract_protocol:
TruSeq RNA Stranded Sample Preparation (Illumina)
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Sequencing libraries were prepared from total RNA using a poly-A selection and either the TruSeq unstranded RNA Sample Preparation (Illumina), TruSeq Stranded RNA Sample Preparation (Illumina) or the KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

value: acute myeloid leukemia


title: 14H031 [re-analysis]

description: reanalysis of GSM1636928


title: P14 CD8+ T cells sgZc3h12a, Day14

description: Library name: N5

value: spleen


title: P14 CD8+ T cells sgBcor, Day14

description: Library name: BT

value: P14 CD8+ T cell


title: 14H019 [re-analysis]

description: reanalysis of GSM1636924

source_name: Heparinised blood

value: Heparinised blood


title: P14 CD8+ T cells sgControl, Day14

description: Library name: KRT8

value: T cell


title: 14H017 [re-analysis]

description: reanalysis of GSM1636923

value: reverse


title: DAOY ZIKV infection 12 hours post infection replicate 3

description:
Medulloblastoma cell line (DAOY) infected for 12 hours with ZIKV (Strain KU365779.1)
DY_Z12_3

value: Infection with ZIKV (Strain KU365779.1) for 12 hours


title: 14H027 [re-analysis]

description: reanalysis of GSM1636927

value: Bone marrow


title: P14 CD8+ T cells sgBcor/Zc3h12a, Day14, Replicate2

description: Library name: A42

data_processing:
Sequencing reads were trimmed by cutadapt (version 1.18) with parameter -m 20 -e 0.1 -O 3 -q 20 --quality-base=33 to remove low-quality bases and adaptor sequences. Trimmed reads were aligned to mouse reference genome (mm10) using bowtie2 aligner (version 2.3.3.1) with parameters –N1-L25 --no-mixed --no-discordant. Reads in blacklist regions defined in the ENCODE blacklist were excluded from downstream analysis. Duplicates were labeled by Picard MarkDuplicates (version 2.20.4) and removed by samtools (version 1.6) view –F 1024. The TSS enrichment was performed to examine the sequencing quality and was computed as the ratio of the average read intensity within TSS +/- 2kb region to that across the genome. Technical replicates of each batch were merged, and Tn5 accessible site were identified by MACS2 callpeak (version 2.1.2) with parameter –g mm -q 0.05 –nomodel --nolambda.
Assembly: mm10
Supplementary files format and content: bigWig for each sample

extract_protocol:
Control, BCOR-deficient, ZC3H12A-deficient and BCOR/ZC3H12A-deficient P14 cells were transferred into Cas9+ B6 mice that were infected with LCMV Clone 13 one day before cell transfer. Fourteen days after transfer, Thy1.1+ or GFP+ P14 cells from spleen were sorted by a S3e cell sorter with purity > 98%. Cells were resuspended and washed with ice cold PBS for 2 times before permeabilization, and Tn5 tagmentation. To permeabilize cells, the cell pellets were resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 10 min. Afterwards, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the samples mixed by inverting the containing tubes for six times. Nuclei were then centrifuged for 10 min at 1000 r.c.f. in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed, nuclei were incubated with Tn5 transposases and tagmentation buffer at 37°C for 30min (Novoprotein, N248). After tagmentation, stop buffer was added directly into the reaction. Samples were incubated at 55°C for 30min to terminate the tagmentation.
Tagmentation products were purified by 2× VAHTS DNA Clean Beads. PCR was performed to amplify the library for 5 cycles using KAPA HiFi PCR Kit (Kapa Biosystems, kk2102) with the following PCR conditions: 72°C for 5min; 98°C for 3mins; and thermocycling at 98°C for 20s, 63°C for 30s. To determine the optimal amplification for each sample, 5ul PCR mix was diluted with 5ul H2O and combined with 2x SYBR qPCR supermix (Novoprotein, E096) to perform qPCR with following conditions: 98°C for 3mins; and thermocycling for 30 cycles at 98°C for 20s, 63°C for 30s and 72°C for 1mins. The additional number of PCR rounds (N) was determined as the qPCR cycle that reached the 1/3 maximum abundance on qPCR amplification curve. All samples were amplified for another N+3 cycles with the following PCR conditions: 98°C for 3mins; thermocycling at 98°C for 20s, 63°C for 30s and 72°C for 3min; and 72°C for 5mins for final extension. The library was sequenced on Illumina NovaSeq.


title: 14H012 [re-analysis]

description: reanalysis of GSM1636921


title: 14H015 [re-analysis]

description: reanalysis of GSM1636922


title: DAOY ZIKV infection 12 hours post infection replicate 1

description:
Medulloblastoma cell line (DAOY) infected for 12 hours with ZIKV (Strain KU365779.1)
DY_Z12_1

value: DAOY


title: P14 CD8+ T cells sgBcor/Zc3h12a, Day14, Replicate1

description: Library name: A41


title: 14H001 [re-analysis]

description: reanalysis of GSM1636919


title: 14H007 [re-analysis]

description: reanalysis of GSM1636920


title: 13H186 [re-analysis]

description: reanalysis of GSM1636918


title: 22Rv1, MARK3i, Replicate4

city: Sangareddy

first: Rajnikant

last: Raut

state: Telangana

address: IITH Road, Near NH65, Kandi

department: Biotechnology

country: India

institute: Indian Institute of Technology Hyderabad

data_processing:
Raw fastq files were processed and aligned to the Hg38 genome assembly and quantified with featureCounts. Count matrix was then utilized to perform differential gene expression analysis with DESeq2 package in R Studio.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes raw count for each samples

extract_protocol: Please see methods


title: 13H185 [re-analysis]

description: reanalysis of GSM1636917


title: P14 CD8+ T cells sgBcor, Day14, Replicate2

description: Library name: A32


title: 22Rv1, MARK3i, Replicate3


title: DAOY ZIKV infection 18 hours post infection replicate 1

description:
Medulloblastoma cell line (DAOY) infected for 18 hours with ZIKV (Strain KU365779.1)
DY_Z18_1

value: Medulloblastoma


title: 13H159 [re-analysis]

description: reanalysis of GSM1636914


title: P14 CD8+ T cells sgBcor, Day14, Replicate1

description: Library name: A31


title: 13H169 [re-analysis]

description: reanalysis of GSM1636915


title: 13H158 [re-analysis]

description: reanalysis of GSM1636913


title: 22Rv1, MARK3i, Replicate2


title: P14 CD8+ T cells sgZc3h12a, Day14, Replicate2

description: Library name: A22


title: 22Rv1, MARK3i, Replicate1


title: 13H141 [re-analysis]

description: reanalysis of GSM1636911


title: DAOY ZIKV infection 12 hours post infection replicate 2

description:
Medulloblastoma cell line (DAOY) infected for 12 hours with ZIKV (Strain KU365779.1)
DY_Z12_2


title: P14 CD8+ T cells sgZc3h12a, Day14, Replicate1

description: Library name: A21


title: 22Rv1, Control, Replicate4


title: P14 CD8+ T cells sgControl, Day14, Replicate2

description: Library name: A12


title: 13H114 [re-analysis]

description: reanalysis of GSM1636908


title: 22Rv1, Control, Replicate3


title: 13H120 [re-analysis]

description: reanalysis of GSM1636909


title: 13H110 [re-analysis]

description: reanalysis of GSM1636907


title: 13H107 [re-analysis]

description: reanalysis of GSM1636906


title: P14 CD8+ T cells sgControl, Day14, Replicate1

description: Library name: A11


title: 13H179 [re-analysis]

description: reanalysis of GSM1636916

source_name: EDTA Blood

value: EDTA Blood


title: Npc1-/-Sting1-/- cerebellum 2

city: Dallas

last: Yan

state: TX

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

description: Library name: NPC1DKO2

data_processing:
RNA-seq data is processed with Astrocyte RNASeq Analysis Workflow on UTSW BioHPC.
snRNA-seq libraries were sequenced using an Illumina NovaSeq 6000. Reads were aligned to the mouse reference mm10 2020-A using CellRanger 7 software (10x Genomics).
Assembly: GRCh38, GRCm38
Supplementary files format and content: CellRanger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: nuclear RNA

source_name: Brain

extract_protocol:
The total RNA was first extracted using TRI Reagent, followed by a clean up with RNeasy plus mini. All steps were done according to manufacturer's protocol. Nuclei were isolated from frozen cerebella as described previously 53. Briefly, cerebellum tissues were homogenized in 2 mL of ice-cold Nuclei EZ lysis buffer (MilliporeSigma, cat # EZ PREP NUC-101) using Dounce homogenizers. Nuclei were centrifuged at 500×g at 4°C for 5 min, washed with ice-cold Nuclei EZ lysis buffer. After wash, the nuclei were resuspended in nuclei suspension buffer (NSB) consisting of 1x PBS, 1% BSA (Thermo Fisher Scientific, cat# AM2618,) and 0.2U/µl RNase inhibitor (Thermo Fisher Scientific, cat# AM2694) and were filtered through a 40-μm Flowmi Cell Strainer (Bel-Art, cat# H13680-0040).
For cerebrum samples, the RNA library was prepared non-stranded with polyA enrichment. For cell line samples, the RNA library was prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's instructions. Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 5’ Reagent Kits (10x Genomics) according to the manufacturer’s protocol.

value: Brain


title: 13H104 [re-analysis]

description: reanalysis of GSM1636905


title: 22Rv1, Control, Replicate1


title: 22Rv1, Control, Replicate2


title: 13H101 [re-analysis]

description: reanalysis of GSM1636904


title: 13H100 [re-analysis]

description: reanalysis of GSM1636903


title: Npc1-/-Sting1-/- cerebellum 1

description: Library name: NPC1DKO1


title: 13H080 [re-analysis]

description: reanalysis of GSM1636901


title: 13H078 [re-analysis]

description: reanalysis of GSM1636900


title: 13H150 [re-analysis]

description: reanalysis of GSM1636912


title: Npc1-/- cerebellum 1

description: Library name: NPC1KO1


title: 13H139 [re-analysis]

description: reanalysis of GSM1636910


title: CD8_miR-379-5p

city: Taichung City

first: Shao-Chun

last: Wang

address: C1-6F., No.350, Jingmao 1st Rd.

department: Cancer Biology and Precision Therapeutics Center

country: Taiwan

institute: China Medical University

data_processing:
The sequencing depth of each sample was > 20 million reads. The reads were aligned with TopHat 2.0.13 to human genome (GRCh38) with default parameters and then were assembled by Cufflink 2.2.1, using Ensembl v90 annotations.
Transcript abundance was measured in TPM.
For the differential expressed genes associated with genotypes, we used fgsea package of R language to perform Gene Set Enrichment Analysis (GSEA) to interpret their biological functions. The significant functions were identified by p < 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes TPM values for each samples

source_name: lymhpocyte

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Life Technologies) following the manufacturer’s instructions.
A total of 1 μg of RNA was used for library preparation. The libraries of RNA-seq were prepared by the Illumina® library preparation kits (TruSeq RNA Library Prep Kit v2) and were sequenced using Illumina NovaSeq to obtain 150-bp paired-end reads.

value: lymhpocyte

value: primary

value: CD8 T cell

value: treated with anti-CD3/CD28 conjugated microbeads (1:200) and IL-2 (100U/mL) for 12 Days.  The cells were transfected with miR-379-5p by electroporation. RNA were isolated after transfection 48 hours.


title: Npc1-/- cerebellum 2

description: Library name: NPC1KO2


title: CD8_miR-Scr

value: WT

value: treated with anti-CD3/CD28 conjugated microbeads (1:200) and IL-2 (100U/mL) for 12 Days.  The cells were transfected with miR-Scr by electroporation. RNA were isolated after transfection 48 hours.


title: 13H073 [re-analysis]

description: reanalysis of GSM1636899

value: acute myeloid leukemia


title: 13H056 [re-analysis]

description: reanalysis of GSM1636897


title: 13H065 [re-analysis]

description: reanalysis of GSM1636898


title: 13H053 [re-analysis]

description: reanalysis of GSM1636896


title: CD8_exhausted

value: treated with anti-CD3/CD28 conjugated microbeads (1:200) and IL-2 (100U/mL), at Day12


title: CD8_naive

value: treated with anti-CD3/CD28 conjugated microbeads (1:200) and IL-2 (100U/mL), at Day0


title: Npc1+/+ cerebellum 2

description: Library name: NPC1WT2


title: 13H048 [re-analysis]

description: reanalysis of GSM1636895

value: Heparinised blood


title: Npc1+/+ cerebellum 1

description: Library name: NPC1WT1


title: 13H046 [re-analysis]

description: reanalysis of GSM1636894

value: reverse


title: BRCA1 siRNA, +dox, rep 3

city: Birmingham

first: Martin

last: Higgs

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
The European Galaxy server: UseGalaxy.eu
Sequence reads trimmed of adaptor sequences and low-qaulity bases (Qaulity Score <20) using Cutadapt in Galaxy server.
Trimmed sequence reads mapped to hg38 reference genome using Bowtie2 in Galaxy server.
Multiple sequencing lanes were merged using SAM tools merge in Galaxy server.
Read count extraction and normalisation performed using featuresCounts in galaxy server.
Assembly: hg38
Supplementary files format and content: tab delimited normalised
Supplementary files format and content: tab delimited raw

source_name: Cervical

growth_protocol: HeLa Kyoto iCas9 SETD1A gRNA #4 cells were grown in DMEM supplemented with 10% tetracycline-free foetal bovine serum (FBS) and 1% pen/strep at 37 °C, 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy kit with on-column DNase I digestion (Qiagen).
mRNA was isolated using NEB Next Poly(A) mRNA magnetic isolation module following manufacturers protocol. RNA libraries for RNA-Seq were constructed using the NEB Next ultra II directional RNA library prep kit for illumina following manufacturers protocol. Libraries normalised to 16.4 nM RNA.

treatment_protocol: HeLa Kyoto iCas9 SETD1A gRNA #4 cells were treated with siRNA against LacZ (Control), ATM or BRCA1. SETD1A knockout was induced by treatment with 1µg/ml doxycycline for 48 hours. Sterile H2O was used as a negative control.

value: Cervical

value: HeLa Kyoto iCas9 SETD1A gRNA #4

value: epithelial cell

value: SETD1A knockout, BRCA1 knockdown

value: Doxycycline


title: 13H019 [re-analysis]

description: reanalysis of GSM1636892

value: Bone marrow


title: 13H083 [re-analysis]

description: reanalysis of GSM1636902


title: brain, 12M, exercised, 4 week, rep3

city: Shanghai

first: Kai

last: Yang

address: 197 Ruijin 2nd Road, Shanghai, 200025, China

department: Shanghai Institute of Traumatology and Orthopedics

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: Brain12MEXrep3

data_processing:
Raw data were splited to two paired sequence
Two paired reads were trimmed for adaptor sequence
Trimmed sequence reads were mapped to mm10 genomic reference using STAR with TranscriptomeSAM mode
Read count and TPM value extraction were performed with rsem using indexed bam files
Data normalization and analysis were performed in R
Assembly: mm10
Supplementary files format and content: csv files include gene_id, transcript_id(s), length, effective_length, expected_count, TPM and FPKM for each Sample.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Standard mRNA-seq Library Prep Kit (NEB) following manufacture's protocols.

treatment_protocol: 12-months-old mice were subjected to treadmill running for 4 weeks.

value: Brain

value: osteaoblast/osteocyte

tag: strain

tag: Sex

value: Male

tag: developmental stage

value: 12 months

value: treadmill running for 4 weeks


title: BRCA1 siRNA, +dox, rep 2


title: brain, 12M, exercised, 4 week, rep2

description: Library name: Brain12MEXrep2

value: WT


title: 13H009 [re-analysis]

description: reanalysis of GSM1636890

value: acute myeloid leukemia


title: 13H006 [re-analysis]

description: reanalysis of GSM1636889


title: BRCA1 siRNA, +dox, rep 1


title: 12H195 [re-analysis]

description: reanalysis of GSM1636888


title: brain, 12M, exercised, 4 week, rep1

description: Library name: Brain12MEXrep1


title: BRCA1 siRNA, -dox, rep 2

value: BRCA1 knockdown


title: BRCA1 siRNA, -dox, rep 3


title: 12H176 [re-analysis]

description: reanalysis of GSM1636887


title: 12H172 [re-analysis]

description: reanalysis of GSM1636884


title: 12H175 [re-analysis]

description: reanalysis of GSM1636886

source_name: Leukapheresis

value: Leukapheresis


title: 12H173 [re-analysis]

description: reanalysis of GSM1636885


title: brain, 12M, rep2

description: Library name: Brain12Mrep2

value: No treatment


title: brain, 12M, rep3

description: Library name: Brain12Mrep3


title: BRCA1 siRNA, -dox, rep 1


title: 13H039 [re-analysis]

description: reanalysis of GSM1636893

value: reverse


title: ATM siRNA, +dox, rep 3

value: Cervical

value: SETD1A knockout, ATM knockdown


title: 12H151 [re-analysis]

description: reanalysis of GSM1636881


title: 12H149 [re-analysis]

description: reanalysis of GSM1636880


title: brain, 12M, rep1

description: Library name: Brain12Mrep1


title: ATM siRNA, +dox, rep 2

value: HeLa Kyoto iCas9 SETD1A gRNA #4

value: epithelial cell


title: 12H171 [re-analysis]

description: reanalysis of GSM1636883


title: brain, 2M, rep3

description: Library name: Brain2Mrep3

value: 2 months


title: 13H018 [re-analysis]

description: reanalysis of GSM1636891

value: Heparinised blood


title: ATM siRNA, +dox, rep 1

value: Doxycycline


title: brain, 2M, rep2

description: Library name: Brain2Mrep2

value: Brain

value: osteaoblast/osteocyte


title: 12H139 [re-analysis]

description: reanalysis of GSM1636879


title: 12H138 [re-analysis]

description: reanalysis of GSM1636878


title: 12H117 [re-analysis]

description: reanalysis of GSM1636876

value: Bone marrow


title: ATM siRNA. - dox, rep 3

value: ATM knockdown


title: 12H124 [re-analysis]

description: reanalysis of GSM1636877


title: 12H116 [re-analysis]

description: reanalysis of GSM1636875


title: bone, 12M, exercised, 4 week, rep3

description: Library name: Bone12MEXrep3

source_name: Cortical bone

value: Cortical bone

value: Male

value: 12 months

value: WT

value: treadmill running for 4 weeks


title: brain, 2M, rep1

description: Library name: Brain2Mrep1

value: No treatment


title: 12H106 [re-analysis]

description: reanalysis of GSM1636874

value: acute myeloid leukemia

value: reverse


title: ATM siRNA. - dox, rep 2

value: Cervical

value: HeLa Kyoto iCas9 SETD1A gRNA #4


title: bone, 12M, exercised, 4 week, rep2

description: Library name: Bone12MEXrep2


title: 12H091 [re-analysis]

description: reanalysis of GSM1636872


title: bone, 12M, exercised, 4 week, rep1

description: Library name: Bone12MEXrep1


title: 12H079 [re-analysis]

description: reanalysis of GSM1636871


title: 12H067 [re-analysis]

description: reanalysis of GSM1636870


title: 12H096 [re-analysis]

description: reanalysis of GSM1636873


title: 12H058 [re-analysis]

description: reanalysis of GSM1636869


title: 12H056 [re-analysis]

description: reanalysis of GSM1636868


title: 12H055 [re-analysis]

description: reanalysis of GSM1636867


title: bone, 12M, rep2

description: Library name: Bone12Mrep2


title: 12H033 [re-analysis]

description: reanalysis of GSM1636865


title: 12H039 [re-analysis]

description: reanalysis of GSM1636866


title: Control siRNA, +dox, rep 2

value: epithelial cell

value: SETD1A knockout, LacZ knockdown


title: bone, 12M, rep1

description: Library name: Bone12Mrep1


title: Control siRNA, +dox, rep 3

value: Doxycycline


title: Control siRNA, -dox, rep 3

value: LacZ knockdown


title: bone, 2M, rep3

description: Library name: Bone2Mrep3

value: osteaoblast/osteocyte

value: 2 months


title: Control siRNA, +dox, rep 1


title: Control siRNA, -dox, rep 2


title: 12H010 [re-analysis]

description: reanalysis of GSM1636862

value: Bone marrow


title: bone, 2M, rep2

description: Library name: Bone2Mrep2

value: Cortical bone


title: 12H007 [re-analysis]

description: reanalysis of GSM1636861

value: Heparinised blood


title: ATM siRNA. - dox, rep 1

value: ATM knockdown


title: 11H240 [re-analysis]

description: reanalysis of GSM1636860


title: Control siRNA, -dox, rep 1


title: bone, 12M, rep3

description: Library name: Bone12Mrep3

value: Male

value: 12 months

value: WT


title: FGO_H2A.ZmKO_H3K27me3_rep2

first: Yu

last: Zhang

address: 138 Yi Xue Yuan Road

institute: Fudan university

description: Library name: Sample 16

data_processing:
Basecalls performed using CASAVA version 1.8. Sequencing reads were trimmed with cutadapt v1.18 and then mapped to the mm9 genome by Bowtie2 (version 2.2.2) with the parameter: –t –q –N 1 –L 25 (Langmead and Salzberg, 2012)., replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Oocyte

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
STAR ChIP-seq was performed following the previously described protocol(Zhang et al., 2016). Briefly, samples were directly lysed and fragmented by MNase at 37°C for 5 minutes, before being incubated with the primary antibody (H2A.Z, abcam, 4174;H3K36me3, Active Motif, 61021; H3K4me3(Zhang et al., 2016); H3K27me3, Diagenode, C15410069; H3K27ac, Active Motif, 39133) overnight with rotation at 4°C. The next day, 100 μg protein A dynabeads (Life Technologies) were added to each sample and incubated for 2-3 h with rotation at 4 °C. The beads were washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 27 μl ddH2O and 1 μl 10× Ex-Taq buffer (TaKaRa). 1 μl proteinase K (Roche, 10910000) was added to each sample and incubated at 55 °C for 90 min to elute DNA from beads. After incubation at 80°C for 40min to inactivate the proteinase K, individual sample was subjected to TELP library preparation without DNA purification

value: Oocyte

tag: chip antibody

value: Full grown oocyte


title: 11H231 [re-analysis]

description: reanalysis of GSM1636857

value: acute myeloid leukemia

value: reverse


title: 11H217 [re-analysis]

description: reanalysis of GSM1636856


title: SOX9_treat_pileup

city: Jinan

first: Hanlin

last: Ma

address: 107 Wenhua Xi Road, Jinan, China.

institute: Qilu Hospital of Shandong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 was used to call peaks with qvalue < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
Peaks were annotated by ChIPseeker package.
Assembly: hg38
Supplementary files format and content: bw

growth_protocol: RPMI 1640 medium, 10% fetal bovine serum, 1% penicillin/streptomycin. Cell were grown in a humidified incubator at 37°C with 5% CO2

extract_protocol:
Cells were harvested and crosslinker with 1% formaldehyde for 10 min at room temperature. After sonication, immunoprecipitation was performed with SOX9 Rabbit Ab (Sigma-Aldrich, AB5535). The immunoprecipitated complex was washed, and DNA was extracted and purified by MinElute PCR Purification Kit (QIAGEN, #28006).
The ChIP-Seq library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, #TD501) according to the manufacturer’ s instructions. For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end.

value: Human ovarian cancer


title: 11H232 [re-analysis]

description: reanalysis of GSM1636858


title: 12H021 [re-analysis]

description: reanalysis of GSM1636864


title: 11H187 [re-analysis]

description: reanalysis of GSM1636854


title: FGO_H2A.ZmKO_H3K27me3_rep1

description: Library name: Sample 15


title: Input_treat_pileup


title: 12H012 [re-analysis]

description: reanalysis of GSM1636863


title: human_CD8_D12

data_processing:
To remove technical sequences, pass-filter data in FASTQ format were processed using Trimmomatic (v0.30) to obtain high-quality clean data.
The data processing included the following steps: removing adapter sequences, trimming 5’ or 3’ end bases that contain N's or have quality values below 20, removing bases with an average quality score below 20 using a sliding window of 4 bp, and discarding reads that are less than 18 bp long after trimming.
According to miRDeep2, a software for discovering known and novel miRNAs from deep sequencing data, we identified all miRNAs and their expression levels.
Differential expression analysis was conducted using the edgeR Bioconductor package (v3.19).
MiRNAs with a false discovery rate (FDR) below 0.001 were considered differentially expressed after statistical testing with the negative binomial distribution.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts and TPM values for each samples

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Life Technologies) following the manufacturer’s instructions.
A total of 1 μg of RNA was used for library preparation. First, the 3' SR Adaptor for Illumina was ligated to the small RNA using a 3' Ligation Enzyme. To prevent adaptor-dimer formation, excess 3' SR Adaptor was hybridized with the SR RT Primer for Illumina. Next, the 5' SR Adaptor for Illumina was ligated to the small RNA using a 5' Ligation Enzyme, and first-strand cDNA was synthesized using ProtoScript II Reverse Transcriptase. Each sample was then amplified by PCR using P5 and P7 primers. The PCR products were purified using DNA clean beads, and the purified products ranging from 140-160 bp were recovered and cleaned up using PAGE.

value: lymhpocyte

value: primary

value: CD8 T cell

value: treated with anti-CD3/CD28 conjugated microbeads (1:200) and IL-2 (100U/mL), at Day12


title: FGO_control_H3K27me3_rep2

description: Library name: Sample 14

value: wild-type


title: 11H183 [re-analysis]

description: reanalysis of GSM1636852

value: Bone marrow


title: 11H177 [re-analysis]

description: reanalysis of GSM1636851


title: 11H234 [re-analysis]

description: reanalysis of GSM1636859


title: FGO_control_H3K27me3_rep1

description: Library name: Sample 13


title: 11H175 [re-analysis]

description: reanalysis of GSM1636850


title: 11H157 [re-analysis]

description: reanalysis of GSM1636849


title: I007_024_combined_libraries

city: Heidelberg

first: Konstantin

last: Okonechnikov

state: Germany

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center

data_processing:
10X data: reads aligned, assigned to cells and gene expression counts computed with CellRanger v2.1.0
DROP-seq,C1 data: reads aligned with STAR, gene expression counts per cell computed with FeatureCount
Filtering of low quality cells performed with Seurat
Assembly: hg19, mm10
Supplementary files format and content: Gene expression matrix (raw)

source_name: Tumor

extract_protocol:
Nuclei from frozen tissue were isolated using the optimized protocol described on the original article.
See protocol column per each sample.
snRNA-seq

value: Tumor

tag: tumor class

value: PXA

tag: protocol

value: female

tag: tumor location

value: Frontal lobe


title: 11H145 [re-analysis]

description: reanalysis of GSM1636848

value: Heparinised blood


title: FGO_H2A.ZmKO_H3K27ac_rep4

description: Library name: Sample 12

value: H3K27ac (Active Motif, 39133)


title: I007_024_short_library


title: 11H140 [re-analysis]

description: reanalysis of GSM1636847


title: FGO_H2A.ZmKO_H3K27ac_rep3

description: Library name: Sample 11

value: Oocyte


title: 11H138 [re-analysis]

description: reanalysis of GSM1636846


title: 12H170 [re-analysis]

description: reanalysis of GSM1636882


title: I007_024_standard_library


title: 11H135 [re-analysis]

description: reanalysis of GSM1636845


title: 11H192 [re-analysis]

description: reanalysis of GSM1636855


title: FGO_H2A.ZmKO_H3K27ac_rep2

description: Library name: Sample 10

value: Full grown oocyte


title: 11H127 [re-analysis]

description: reanalysis of GSM1636843

value: acute myeloid leukemia


title: 11H132 [re-analysis]

description: reanalysis of GSM1636844

value: reverse


title: ICGC_PA74_combined_libraries

value: PA

value: male

value: Cerebellum


title: FGO_control_H3K27ac_rep4

description: Library name: Sample 9


title: human_CD8_D0

value: lymhpocyte

value: primary

value: CD8 T cell

value: WT

value: treated with anti-CD3/CD28 conjugated microbeads (1:200) and IL-2 (100U/mL), at Day0


title: 11H103 [re-analysis]

description: reanalysis of GSM1636842


title: 11H097 [re-analysis]

description: reanalysis of GSM1636841


title: ICGC_PA74_short_library

value: Tumor


title: FGO_control_H3K27ac_rep3

description: Library name: Sample 8

value: wild-type


title: ICGC_PA74_standard_library


title: FGO_control_H3K27ac_rep2

description: Library name: Sample 7


title: ICGC_PA56_NovaSeq6000


title: 11H014 [re-analysis]

description: reanalysis of GSM1636836

value: Bone marrow


title: SN_H2AZ_rep2

description: Library name: Sample 6

value: Full grown oocyte (surrounded nucleolus)


title: ICGC_GBM61_NovaSeq6000

value: GBM

value: female

value: Hemispheric


title: 11H010 [re-analysis]

description: reanalysis of GSM1636835

value: Heparinised blood

value: acute myeloid leukemia


title: SN_H2AZ_rep1

description: Library name: Sample 5

value: Oocyte


title: 11H035 [re-analysis]

description: reanalysis of GSM1636839

value: reverse


title: 11H002 [re-analysis]

description: reanalysis of GSM1636834


title: 11H027 [re-analysis]

description: reanalysis of GSM1636838


title: 10H174 [re-analysis]

description: reanalysis of GSM1636833


title: sh NFKBIZ 24h S.a. treated biol rep3

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
CLC Genomics Workbench (v24.0)
Raw sequence reads were trimmed for low quality- and adapter sequences using CLC tool "Trim reads" (quality limit 0,05)
Read count extraction and Normalization were performed using CLC Genomics Workbench (Expression values = TPM)
Assembly: GRCh38.109
Supplementary files format and content: tab delimited  text files include raw counts, RPKM and TPM

source_name: fore skin

growth_protocol: Primary human keratinocytes were maintained in CnT-07 epithelial proliferation medium (CELLnTEC) with respective supplements and antibiotics in humified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested 24h post treatment using TRIzol extraction
Barcoded mRNA seq libraries were prepared from 200 ng total RNA at Novogene (Cambridge; UK). The mRNA present in the total RNA sample was isolated with magnetic beads of oligos d(T)25. This method is known as polyA-tailed mRNA enrichment. Subsequently, mRNA was randomly fragmented and cDNA synthesis proceeds through the use of random hexamers and the reverse transcriptase enzyme. Once the synthesis of the first chain is finished, the second chain is synthesized with the addition of an Illumina buffer. With this and together with the presence of dNTPs, RNase H and polymerase I from E.coli, the second chain is obtained by Nick translation. The resulting products go through purification, end-repair, A-tailing and adapter ligation. Fragments of the appropriate size are enriched by PCR, where indexed P5 and P7 primers are introduced, and final products are purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection. Quantified libraries have been pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount. Sequencing strategy was paired-end 150 cycles (PE150).

treatment_protocol: Terminal differentiation was induced for 72h with 2mM CaCl2 in supplemented medium. The day prior treatment cells were starved in CnT-07 without supplements, antibiotics or the addition of CaCl2. Infection with S. aureus for 1h (MOI30; MRSA strain USA300 WT LAC), washed and further incubation 23h post infection with non-supplemented Cn-07 medium with antibiotics. Treatment for 24h with muramyl-dipeptide (MDP-LD; 20µg/mL, transfected with ProteoJuice) in non-supplemented Cn-07 medium, without antibiotics.

value: fore skin

value: primary human keratinocytes

value: keratinocytes

value: NFKBIZ KD

value: differentiated, S.a. 1h + 23h


title: NSN_H2AZ_rep2

description: Library name: Sample 4

value: Full grown oocyte (non- surrounded nucleolus)


title: 10H173 [re-analysis]

description: reanalysis of GSM1636832


title: NSN_H2AZ_rep1

description: Library name: Sample 3


title: 10H130 [re-analysis]

description: reanalysis of GSM1636829


title: D7GO_control_H2A.Z_rep2

description: Library name: Sample 2

value: Growing oocyte D7


title: 10H106 [re-analysis]

description: reanalysis of GSM1636828


title: sh NFKBIZ 24h MDP treated, biol rep3

value: differentiated, MDP 24h


title: 10H087 [re-analysis]

description: reanalysis of GSM1636827


title: 11H017 [re-analysis]

description: reanalysis of GSM1636837

value: Bone marrow


title: 10H078 [re-analysis]

description: reanalysis of GSM1636826

value: Leukapheresis


title: 11H044 [re-analysis]

description: reanalysis of GSM1636840


title: D7GO_control_H2A.Z_rep1

description: Library name: Sample 1

value: wild-type


title: 10H070 [re-analysis]

description: reanalysis of GSM1636825


title: sh NFKBIZ 24h MDP treated, biol rep2


title: LCMVc13 infection, WT, D5, rep3

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

data_processing:
Read quality was assessed and low quality reads trimmed with fastp.
Trimmed reads were mapped to the mouse genome (mm10) using bowtie2, with standard parameters.
Picard was used to remove PCR duplicates. The deduplicated reads were then filtered to remove mitochondrial chromosome, Y chromosome, improperly paired and non-mapping reads using samtool flags.
Peak summits were called using macs2 using parameter --nomodel, --keep-dup all and --call-summits.
Identification of differentially accessible regions (at least a 1-fold-change and false discovery rate less than 0.05) was performed using DiffBind package.
Assembly: mm10
Supplementary files format and content: bigwig files for each sample

extract_protocol:
Nuclei were washed and resuspended in 50 μL 1× TDE1 buffer (Illumina) containing 2.5 μL TDE1 transposase (Illumina). The transposase reaction was conducted at 37 °C for 30 min, with mild shaking.
Library amplification and barcoding were performed with NEBNext Ultra II Q5 Master Mix (New England Biolabs) using IDT dual index primer set (Integrated DNA Technologies). PCR was conducted for 10–11 cycles. Library purification was performed with the MinElute PCR Purification Kit (Qiagen) and library size distribution was assessed using the TapeStation High Sensitivity DNA Kit (Agilent).

treatment_protocol: 50,000 sorted P14 CD8+ T cells were lysed to extract nuclei using cell lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% tween-20, 0.1% IGEPAL CA-630, 0.01% digitonin and 1% bovine serum albumin).

value: spleen

value: CD8+ T cells


title: sh NFKBIZ 24h MDP treated, biol rep1


title: LCMVc13 infection, WT, D5, rep2


title: sh NFKBIZ 24h S.a. treated biol rep2


title: 10H053 [re-analysis]

description: reanalysis of GSM1636823

value: Heparinised blood


title: 10H066 [re-analysis]

description: reanalysis of GSM1636824

value: acute myeloid leukemia


title: 10H051 [re-analysis]

description: reanalysis of GSM1636822


title: sh NFKBIZ 24h untreated, biol rep3

value: differentiated, untreated


title: 10H048 [re-analysis]

description: reanalysis of GSM1636821

value: reverse


title: 10H149 [re-analysis]

description: reanalysis of GSM1636831


title: 10H040 [re-analysis]

description: reanalysis of GSM1636820


title: LCMVc13 infection, WT, D5, rep1


title: 10H136 [re-analysis]

description: reanalysis of GSM1636830


title: sh NFKBIZ 24h S.a. treated biol rep1

value: fore skin


title: sh NFKBIZ 24h untreated, biol rep2

value: primary human keratinocytes


title: 10H034 [re-analysis]

description: reanalysis of GSM1636819


title: LCMVc13 infection,GFI1-KO, D5, rep3


title: sh NFKBIZ 24h untreated, biol rep1

value: keratinocytes


title: sh control 24h S.a. treated, biol rep3

value: ctrl


title: LCMVc13 infection,GFI1-KO, D5, rep1


title: 10H015 [re-analysis]

description: reanalysis of GSM1636816


title: 10H014 [re-analysis]

description: reanalysis of GSM1636815


title: 10H007 [re-analysis]

description: reanalysis of GSM1636814


title: sh control 24h S.a. treated, biol rep2

value: differentiated, S.a. 1h + 23h


title: 10H005 [re-analysis]

description: reanalysis of GSM1636813


title: LCMVc13 infection, WT, D3, rep3


title: sh control 24h S.a. treated, biol rep1


title: 10H029 [re-analysis]

description: reanalysis of GSM1636818


title: 09H106 [re-analysis]

description: reanalysis of GSM1636810


title: 09H119 [re-analysis]

description: reanalysis of GSM1636811


title: sh control 24h MDP treated, biol rep2


title: LCMVc13 infection, WT, D3, rep2


title: 10H026 [re-analysis]

description: reanalysis of GSM1636817


title: 09H102 [re-analysis]

description: reanalysis of GSM1636809


title: LCMVc13 infection,GFI1-KO, D5, rep2


title: LCMVc13 infection, WT, D3, rep1


title: 09H092 [re-analysis]

description: reanalysis of GSM1636807


title: sh control 24h MDP treated, biol rep3


title: 09H094 [re-analysis]

description: reanalysis of GSM1636808


title: LCMVc13 infection,GFI1-KO, D3, rep2


title: 09H090 [re-analysis]

description: reanalysis of GSM1636806


title: 09H088 [re-analysis]

description: reanalysis of GSM1636804


title: LCMVc13 infection,GFI1-KO, D3, rep1


title: 09H084 [re-analysis]

description: reanalysis of GSM1636802


title: bone, 2M, rep1

description: Library name: Bone2Mrep1

value: Cortical bone

value: osteaoblast/osteocyte

value: Male

value: 2 months

value: WT

value: No treatment


title: 09H089 [re-analysis]

description: reanalysis of GSM1636805

value: Bone marrow


title: 09H085 [re-analysis]

description: reanalysis of GSM1636803


title: LCMVc13 infection,GFI1-KO, D3, rep3

value: spleen

value: CD8+ T cells


title: 09H079 [re-analysis]

description: reanalysis of GSM1636801

value: Heparinised blood

value: acute myeloid leukemia


title: sh control 24h untreated, biol rep3

value: differentiated, untreated


title: sh control 24h untreated, biol rep2

value: fore skin


title: 10H001 [re-analysis]

description: reanalysis of GSM1636812

value: reverse


title: 09H078 [re-analysis]

description: reanalysis of GSM1636800


title: BAT_aMKO_bio rep 4

city: Noda

first: Yoshikazu

last: Higami

state: Chiba

address: 2641, Ymazaki

department: Faculty of Pharmaceutical Science

country: Japan

institute: Tokyo University of Science

data_processing:
The RNA-seq reads were aligned to the mouse reference genome GRCm39 was calculated using STAR (v2.711a) two-pass alignment (Dobin A et al. 2013, Dobin A et al, 2015).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: brown adipose tissue

extract_protocol:
Total RNA was extracted from WAT and BAT from 30-week-old aMKO mice using the Relie PrepTM RNA Tissue Miniprep System (Promega, WI, USA) according to the manufacturer’s protocol.
Library preparation and RNA sequencing were done by Novogene Co., Ltd. (Beijing, China).

value: brown adipose tissue

value: adipocyte-specific Mipep Knockout


title: 09H070 [re-analysis]

description: reanalysis of GSM1636799


title: sh control 24h untreated, biol rep1

value: primary human keratinocytes

value: keratinocytes

value: ctrl


title: sh control 24h MDP treated, biol rep1

value: differentiated, MDP 24h


title: BAT_aMKO_bio rep 2


title: BAT_aMKO_bio rep 3


title: 09H062 [re-analysis]

description: reanalysis of GSM1636798


title: 09H058 [re-analysis]

description: reanalysis of GSM1636796


title: 09H060 [re-analysis]

description: reanalysis of GSM1636797


title: CMK cells, no treated, replicate 2

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome and GENCODE v29 using STAR 2.7.10a with parameters --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using stringtie v2.1.7. Gene differential expression were calculated using DESeq2 v1.40.2. Alternative splicing events were called using rMATS v4.1.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and expression values of each gene for each sample and differential expression values between treatment group and control group.

source_name: CMK

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; stranded RNA-Seq

value: CMK

value: AMKL cells

value: No treated


title: 09H057 [re-analysis]

description: reanalysis of GSM1636795

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations, using both stranded and unstranded parameters for samples sequenced using stranded libraries.
Strand orientation is reverse for stranded samples, that is R1 aligns on the reverse gene orientation.
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM


title: CMK cells, indisulam treated,5μmol, replicate 2

value: Treated by indisulam


title: 09H045 [re-analysis]

description: reanalysis of GSM1636793


title: CMK cells, no treated, replicate 1


title: 09H042 [re-analysis]

description: reanalysis of GSM1636792

value: Bone marrow


title: BAT_contorol_bio rep 4

value: control


title: BAT_contorol_bio rep 3


title: CMK cells, indisulam treated, 5μmol, replicate 1


title: BAT_contorol_bio rep 2


title: 09H048 [re-analysis]

description: reanalysis of GSM1636794


title: MDAMB231 48 hour IL4 #3

city: Nashville

first: Demond

last: Williams

state: TN

address: 715 CA Preston Research Building 2220 Pierce Avenue

department: Cancer Biology

institute: Vanderbilt University

data_processing:
Analysis was performed following the Illumina Dragen pipeline for RNASeq
Assembly: hg38
Supplementary files format and content: SigGenesList

growth_protocol: MDAMB231 Cells were grown in DMEM with 10% FBS at 5% CO2 at 37 celcius

extract_protocol:
RNA was extracted using Zymogen Quick Rna Miniprep kit
Library was constructed using NEBNext poly(A) selection library kit

treatment_protocol: Cytokine stimulation was performed by adding 10ng recombinant human IL4 to medium for the indicated time.

value: Mammary Gland Adenocarcinoma

value: WT

value: 10ng IL4

tag: time point

value: 48 Hours


title: 11H186 [re-analysis]

description: reanalysis of GSM1636853

value: acute myeloid leukemia

value: reverse


title: 09H015 [re-analysis]

description: reanalysis of GSM1636788


title: 09H022 [re-analysis]

description: reanalysis of GSM1636789


title: 09H026 [re-analysis]

description: reanalysis of GSM1636791


title: 09H024 [re-analysis]

description: reanalysis of GSM1636790

value: Heparinised blood


title: MDAMB231 48 hour IL4 #2


title: 09H008 [re-analysis]

description: reanalysis of GSM1636786


title: BAT_contorol_bio rep 1

value: brown adipose tissue


title: MDAMb231 48 hour IL4 #1


title: 09H005 [re-analysis]

description: reanalysis of GSM1636785


title: WAT_aMKO_bio rep 4

source_name: genital white adipose tissue

value: genital white adipose tissue

value: adipocyte-specific Mipep Knockout


title: BAT_aMKO_bio rep 1


title: WAT_aMKO_bio rep 3


title: MDAMB231 24 hour IL4 #3

value: 24 Hours


title: 09H002 [re-analysis]

description: reanalysis of GSM1636784


title: 08H138 [re-analysis]

description: reanalysis of GSM1636783


title: MDAMB231 24 hour IL4 #2


title: 08H137 [re-analysis]

description: reanalysis of GSM1636782


title: WAT_aMKO_bio rep 2


title: 08H104 [re-analysis]

description: reanalysis of GSM1636779


title: MDAMB231 24 hour IL4 #1


title: 08H108 [re-analysis]

description: reanalysis of GSM1636780


title: 08H089 [re-analysis]

description: reanalysis of GSM1636778


title: 09H013 [re-analysis]

description: reanalysis of GSM1636787


title: WAT_contorol_bio rep 4


title: WAT_aMKO_bio rep 1


title: 08H087 [re-analysis]

description: reanalysis of GSM1636776


title: MDAMB231 No cytokine sample #3

value: No Cytokine


title: MDAMB231 No cytokine sample #2


title: 08H082 [re-analysis]

description: reanalysis of GSM1636775


title: 08H088 [re-analysis]

description: reanalysis of GSM1636777


title: 08H065 [re-analysis]

description: reanalysis of GSM1636774


title: MDAMB231 No cytokine sample #1


title: 08H063 [re-analysis]

description: reanalysis of GSM1636773


title: WAT_contorol_bio rep 3


title: WAT_contorol_bio rep 2


title: 08H056 [re-analysis]

description: reanalysis of GSM1636771


title: 08H113 [re-analysis]

description: reanalysis of GSM1636781


title: U2OS, siMITF, UT, rep3

city: Reykjavik

first: Daniel

last: Magnusson

address: Sturlugata 8

department: Biomedical

country: Iceland

institute: Háskóli Íslands

data_processing:
The RNAseq data was analyzed using Kallisto (v 0.43)(27) with Ensembl human transcriptome release-94 as a reference using 30 bootstrap samples.
The abundance estimates of each transcript was then analyzed using Sleuth (v 0.3)(28) and likelihood ratio test used to estimate differential expression and obtain q-values for each transcript
Enriched biological processes were obtained from the online DAVID(29) annotation tool for genes down-regulated on treatment with siMITF (log2 fc ≤ -0.576). The log2 fold change was calculated using the beta estimate value.
Assembly: hg18
Supplementary files format and content: Tab-Seperated Values files containing counts and TPM (transcripts Per million)

molecule: cytoplasmic RNA

source_name: Bone

extract_protocol:
RNA was isolated using TRI reagent (Thermo, AM9738).
The RNA was DNase1 treated (Qiagen) and purified using RNeasy Mini kit (Qiagen)

value: Bone

value: Epithelial

value: Osteosarcoma

value: siMITF, UT


title: WAT_contorol_bio rep 1

value: control


title: 08H055 [re-analysis]

description: reanalysis of GSM1636770

extract_protocol:
TruSeq RNA Stranded Sample Preparation (Illumina)
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Sequencing libraries were prepared from total RNA using a poly-A selection and either the TruSeq unstranded RNA Sample Preparation (Illumina), TruSeq Stranded RNA Sample Preparation (Illumina) or the KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

value: Bone marrow


title: Nsun7-/- mouse 3

city: Vienna

first: Sergey

last: Isaev

address: Spitalgasse, 4

department: Department of Neuroimmunology

country: Austria

institute: Medical University of Vienna

data_processing:
Bulk RNA-Seq quanitification was performed based on raw reads with kallisto (v. 0.50.1). Counts of each isoform of the gene were summirized and rounded (similarly to tximport pipeline) to work on a gene level instead of transcript level.
Assembly: mm39
Supplementary files format and content: tsv-files with estimated counts and TPMs per each isoform

source_name: Testis

extract_protocol:
The collected mouse testes were decapsulated and the obtained seminiferous tubes were used for RNA isolation using ExtractRNA reagent (evrogen) according to the manufacturer's protocol. The isolated RNA was used for rRNA and globin depletion using Illumina Ribo-Zero Plus rRNA Depletion (Illumina).
Libraries were then prepared using the NEBNext® Ultra II RNA Library Prep Kit for Illumina (NEB) with dual indexing (NEB E6445 Set 3 NebNext Dual).

value: Testis

value: 3 month


title: 08H054 [re-analysis]

last: Sauvageau

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description: reanalysis of GSM1636769


title: 08H053 [re-analysis]

description: reanalysis of GSM1636768


title: U2OS, siMITF, 1h, rep3

value: siMITF, 1h


title: 08H050 [re-analysis]

description: reanalysis of GSM1636767

value: acute myeloid leukemia


title: 08H049 [re-analysis]

description: reanalysis of GSM1636766

value: reverse


title: U2OS, si Control, UT, rep3

value: si Control, UT


title: Nsun7-/- mouse 2


title: 08H022 [re-analysis]

description: reanalysis of GSM1636764

value: Heparinised blood


title: Nsun7-/- mouse 1


title: U2OS, siControl, 4h, rep3

value: siControl, 4h


title: U2OS, siControl, 1h, rep3

value: siControl, 1h


title: 08H011 [re-analysis]

description: reanalysis of GSM1636762


title: 08H018 [re-analysis]

description: reanalysis of GSM1636763

source_name: Bone marrow


title: WT mouse 2 - control

value: WT


title: WT mouse 3 - control


title: 07H158 [re-analysis]

description: reanalysis of GSM1636760


title: 08H004 [re-analysis]

description: reanalysis of GSM1636761


title: 07H156 [re-analysis]

description: reanalysis of GSM1636759


title: 08H033 [re-analysis]

description: reanalysis of GSM1636765


title: 08H062 [re-analysis]

description: reanalysis of GSM1636772


title: 07H155 [re-analysis]

description: reanalysis of GSM1636758


title: U2OS, siMITF, 4h, rep3

value: siMITF, 4h


title: 07H152 [re-analysis]

description: reanalysis of GSM1636757


title: U2OS, siMITF, 4h, rep2

value: Bone


title: 07H151 [re-analysis]

description: reanalysis of GSM1636756


title: SP2509, Replicate3

city: Boston

first: Manish

middle: V.

last: Bais

state: MA

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

data_processing:
Proprietary perl script developed by NOVOGENE bioinformatics facility.
Reference genome alignment using HISAT2.
Gene expression quantification using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized count for each samples

source_name: Tongue

extract_protocol:
RNA was isolated using TRIzol and purified with RNeasy Mini kit (Qiagen). Around 400 nanogram of RNA was used for sequencing at NOVOGENE facility.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

value: Tongue


title: SP2509, Replicate2


title: 07H148 [re-analysis]

city: Montreal

first: Guy

description: reanalysis of GSM1636755


title: 07H133 [re-analysis]

description: reanalysis of GSM1636753

source_name: Heparinised blood


title: SP2509 Replicate1


title: U2OS, siControl, 4h, rep2

value: Epithelial

value: Osteosarcoma


title: 07H131 [re-analysis]

description: reanalysis of GSM1636752


title: 07H125 [re-analysis]

description: reanalysis of GSM1636751


title: U2OS, si Control, UT, rep2


title: WT mouse 1 - control


title: Vehicle, Replicate1

value: Vehicle


title: 07H124 [re-analysis]

description: reanalysis of GSM1636750


title: U2OS, siMITF, UT, rep1

value: siMITF, UT


title: 07H117 [re-analysis]

description: reanalysis of GSM1636749

value: Bone marrow


title: 07H107 [re-analysis]

description: reanalysis of GSM1636747


title: 07H098 [re-analysis]

description: reanalysis of GSM1636745


title: U2OS, siMITF, 1h, rep2


title: U2OS, siMITF, 4h, rep1


title: 07H106 [re-analysis]

description: reanalysis of GSM1636746


title: OVX_V 24h IsthUTJ

city: Columbia

first: Wipawee

last: Winuthayanon

state: Missouri

address: 1030 Hitt Street

department: OB/GYN & Women's Health

institute: University of Missouri

description: 100bp read length

data_processing:
For scRNA-seq analysis, the computer was equipped with AMD Ryzen 9 5900X 12-Core Processor, 24 Threads and used as a server using Linux operating system. For PGR ChIP-seq: The model-based analysis of ChIP-sequencing (MACS) peak finding algorithm was used to normalize ChIP against the input control.
Assembly: mm10
Supplementary files format and content: Raw data were processed using CellRanger-6.0.1. Generated loom files were then read in scanpy v1.9.1 using JupyterLab33 for analyses and saved in an h5ad format. For PGR ChIP-seq: .bed file was used as processed file.

source_name: oviduct

extract_protocol:
For scRNA-seq analysis: Wild-type animals were ovariectomized and left for 14 days to recover and be rid of ovarian derived-steroid hormones. Sesame oil (100 μL) was used as a negative (Vehicle or Veh) control group. Progesterone (P4) at a dose of 1 mg was diluted in 100 μL of 10% ethanol and sesame oil. Ovariectomized females were subcutaneously injected with Veh or P4. Two or Twenty-four hours after injection, the oviduct was collected for scRNA-seq analysis. Wnt7aCre/+;Pgrf/f (cKO) mouse models were used in this study. Pgrf/f and PgrCre/+ mice were received from Drs. John Lydon (Baylor College of Medicine) and Francesco DeMayo (National Institute of Environmental Health Sciences). The generation of Wnt7aCre/+ mice is described previously. Genotyping protocols for each mouse strain are described in original publications. Oviducts were collected at 0.5 dpc from Pgrf/f and Wnt7aCre/+;Pgrf/f (n = 8 mice/group). In another group of experiments assessing the role of exogenous P4 in oviduct gene expression, oviducts were collected from ovariectomized females treated with Veh (n = 4 mice) and P4 for 2 h (n = 4 mice) or 24 h (n = 3 mice). Oviducts were pooled and collected in L15 media supplement with 1% fetal bovine serum (L15 + 1%FBS) and placed on ice. The oviduct was dissected into distal (infundibulum with ampulla, referred to as InfAmp) or proximal (isthmus with UTJ, referred to as IsthUTJ) regions. To isolate oviductal cells, oviducts were quickly uncoiled by trimming the mesosalpinx in order to locate the ampulla-isthmus junction (AIJ). Then, the tissues were dissected at the AIJ region for subsequent InfAmp and IsthUTJ cell isolation. After dissection, 0.25% trypsin-EDTA (Sigma, T4049) was injected into the oviduct using a blunted 30.5-gauge needle until the trypsin was visibly flushed out from the other end of the oviduct. The tissues were then placed in a tube containing 500 μL of trypsin and incubated on ice for 30 minutes and at 37°C for another 30 minutes. After the incubation, 500 μL of FBS was added to stop the enzymatic activity of trypsin. Oviductal cells were then flushed out from oviductal tubes with 4°C L15 + 10%FBS. At this stage, the epithelial, stromal, and parts of muscle cell layers were visibly flushed out. Only translucent longitudinal muscle cells were left intact. Cell clumps and tissue debris were strained twice through 40-μm cell strainers. Cells were then spun down and resuspended in 0.04% bovine serum albumin AlbuMax (ThermoFisher Scientific, 11020–021) in phosphate-buffered saline. The final cell concentration was targeted for 8,000 cells/run. For PGR ChIP-seq analysis: The oviducts were collected from C67BL6/J female mice at 2.5 dpc for ChIP-seq analysis (n=8 mice/treatment). The oviducts were flash frozen, and 16 oviducts were pooled per sample. ChIP was performed by Active Motif Inc. (Carlsbad, CA) using an antibody against PGR (sc7208, Santa Cruz Biotechnology, Dallas, TX). ChIP-seq libraries were prepared by Active Motif and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Facility using a NextSeq 500 NGS system.
For scRNA-seq analysis: scRNA-seq libraries were performed using the manufacturer’s protocol (10X Genomics Inc). Single Cell 3’ v2 chemistry was used. Briefly, individual cells (~8,000 cells/run) were separated into droplets by Gel bead in EMulsion (GEM) technology using 10X Chromium Controller. Emulsion beads were broken and barcoded cDNAs were pooled for amplification. Libraries generated were sequenced using an Illumina NovoSeq 6000.

value: oviduct

tag: region

value: isthmus and uterotubal junction

tag: timepoint

value: 24h vehicle (V) treatment


title: 07H095 [re-analysis]

description: reanalysis of GSM1636744

tag: tissue

value: acute myeloid leukemia

value: reverse


title: 07H112 [re-analysis]

description: reanalysis of GSM1636748

value: Heparinised blood

tag: cell type


title: 07H089 [re-analysis]

description: reanalysis of GSM1636743


title: U2OS, siMITF, 1h, rep1

tag: cell line

tag: genotype

value: siMITF, 1h


title: 07H134 [re-analysis]

description: reanalysis of GSM1636754


title: OVX_V 24h InfAmp

description: 100bp read length

value: infundibulum and ampulla


title: 07H082 [re-analysis]

description: reanalysis of GSM1636742


title: Vehicle, Replicate3

tag: treatment


title: U2OS, siControl, 1h, rep2

value: siControl, 1h


title: Vehicle, Replicate2


title: 07H063 [re-analysis]

description: reanalysis of GSM1636741


title: 07H060 [re-analysis]

description: reanalysis of GSM1636740


title: OVX_V 2h IsthUTJ

description: 100bp read length

value: 2h vehicle (V) treatment


title: U2OS, si Control, UT, rep1

value: Bone

value: si Control, UT


title: 07H055 [re-analysis]

description: reanalysis of GSM1636739


title: U2OS, siControl, 4h, rep1

value: Epithelial

value: siControl, 4h


title: U2OS, siControl, 1h, rep1

value: Osteosarcoma


title: 07H043 [re-analysis]

description: reanalysis of GSM1636738


title: OVX_P4 24h IsthUTJ

description: 100bp read length

value: 24h progesterone (P4) treatment


title: 07H034 [re-analysis]

description: reanalysis of GSM1636737

value: Bone marrow


title: OVX_V 2h InfAmp

description: 100bp read length

value: oviduct


title: 07H019 [re-analysis]

description: reanalysis of GSM1636734


title: 07H024 [re-analysis]

description: reanalysis of GSM1636736


title: OVX_P4 24h InfAmp

description: 100bp read length


title: OVX_P4 2h IsthUTJ

description: 100bp read length

value: isthmus and uterotubal junction

value: 2h progesterone (P4) treatment


title: 06H106 [re-analysis]

description: reanalysis of GSM1636732

value: acute myeloid leukemia


title: SVI-003-21 LY6H-positive

city: Parkville

first: Jacqueline

last: Schiesser

address: 50 Flemington Road

institute: Murdoch Childrens Research Institute

data_processing:
Sequenced reads were mapped to the whole human genome (GrCh38 assembly) with the Spliced Transcript Alignment to a Reference (STAR) software (version 2.7.3) using default parameters. Nonuniquely mapping reads and read pairs with unpaired alignments were excluded.
Read counts for each gene were determined using featureCounts as part of the Rsubread VERSION library
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreatic islet

extract_protocol:
Isolated human pancreatic islets were stained with antibodies against LY6H and sorted by FACS using a BD Influx (BD Biosciences) or BD FACSAria Fusion (BD Biosciences). RNA extraction of FACS purified populations was performed using Trizol reagent as directed by the manufacturer (ThermoFisher, 15596026).
RNA libraries were prepared for sequencing using a Truseq Stranded mRNA Library Prep Kit (Illlumina; Donor SVI-015-20) or using a SMARTer Stranded Total RNA-seq Kit v3 - Pico Input Mammalian (Takara; Donor SVI-003-21) as per the manufacters instructions.

value: Pancreatic islet

tag: cell population


title: SVI-003-21 Unsorted

value: Unsorted


title: 06H103 [re-analysis]

description: reanalysis of GSM1636731

value: Heparinised blood

tag: strand orientation

value: reverse


title: OVX_P4 2h InfAmp

description: 100bp read length

value: infundibulum and ampulla

tag: strain


title: SVI-015-20 LY6H-negative


title: 06H143 [re-analysis]

description: reanalysis of GSM1636733


title: 06H089 [re-analysis]

description: reanalysis of GSM1636729


title: WT IsthUTJ 0.5 dpc

description: 100bp read length

value: Pgrf/f

value: f/f

value: 0.5 days post coitus (dpc)


title: 06H099 [re-analysis]

description: reanalysis of GSM1636730


title: 06H077 [re-analysis]

description: reanalysis of GSM1636728


title: 06H075 [re-analysis]

description: reanalysis of GSM1636727


title: SVI-015-20 LY6H-positive


title: SVI-003-21 LY6H-negative


title: 07H020 [re-analysis]

description: reanalysis of GSM1636735


title: 06H074 [re-analysis]

description: reanalysis of GSM1636726


title: 06H073 [re-analysis]

description: reanalysis of GSM1636725


title: WT InfAmp 0.5 dpc

description: 100bp read length


title: SVI-015-20 Unsorted


title: cKO IsthUTJ 0.5 dpc

description: 100bp read length

value: f/f Cre/+


title: shHOXC6_2_3

city: Wuxi City

first: Yonghua

last: Pang

state: Jiangsu Province

address: 101 Xingyuan North Road, North Street

institute: The 904th Hospital of the Joint Logistics Support Force of the People's Liberation Army of China

data_processing:
The sequence fragments were obtained from high-throughput sequencing instrument-generated image data, and were converted into sequence data (reads) through CASAVA base recognition, stored in fastq format files.
Remove reads with adapters, remove reads containing N, and remove low-quality reads (reads where more than 50% of the bases have a Qphred score <= 5)
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Supplementary files format and content: The Excel spreadsheet contains the counts of genes.
Supplementary files format and content: The Excel spreadsheet contains the counts of genes.

source_name: RD-ES

growth_protocol: The RD-ES cells were grown in Dulbecco's Modified Eagle Medium (DMEM) culture medium, supplemented with 10% Fetal Bovine Serum (FBS) in a standard humidified incubator with 5% CO2 at 37°C.

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required

value: RD-ES

value: Ewing sarcoma


title: 06H048 [re-analysis]

description: reanalysis of GSM1636724


title: U2OS, siMITF, UT, rep2

value: Bone

value: Epithelial

value: Osteosarcoma

value: siMITF, UT


title: 06H029 [re-analysis]

description: reanalysis of GSM1636722

value: Bone marrow


title: 06H038 [re-analysis]

description: reanalysis of GSM1636723

value: acute myeloid leukemia


title: B cell, LPS-primed, MSU-treated 2

city: Seongnam

first: Eui Ho

last: Kim

state: Gyeongggi-do

address: 16 Daewangpangyo-ro 712 beon-gil, Bundang-gu

country: South Korea

institute: Institut Pasteur Korea

description:
biol rep 2
NormCounts_B cell.txt
B cell_4-2

data_processing:
Hisat2 v2.1.0 for mapping and alignment, and featureCounts v2.0.3 for counting.
Quality control checks after each step using FastQC 0.11.9 and MultiQC v1.12.
To identify differentially expressed genes (DEGs), raw counts were obtained from the sequencing data. Genes with zero counts across all of the samples were removed to ensure data quality. We then searched for samples with unusual values or outliers using Cook's distance from the DESeq2 1.40.2 package and the Molecular Degree Perturbation (MDP) score from the mdp 1.24.0 package in R.
For the actual differential expression analysis, we used the default parameters of the DESeq2 package.
Assembly: For the analysis, the mouse genome (mm10_NCBI_108) was used along with gene annotations from mm10.refGene.gtf.
Supplementary files format and content: Text files include normalized counts for each sample.

source_name: Spleen

growth_protocol: BMDCs were maintained in RPMI supplemented with GM-CSF, 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃ for 10 days. B cells were isolated from mouse spleen cells using EasySep B cell isolation kit (STEMCELLS TECHNOLOGIES).

extract_protocol:
RNA (6~10μg) was harvested using TRIzol. For B cell RNA, additional steps were performed: DNAase I treatment & inactivation, and RNA precipitation using sodium acetate & EtOH.
TruSeq Stranded mRNA Library Prep Kit was used.

treatment_protocol: Cells were stimulated by treatment of MSU with or without LPS priming (100 ng/mL for 1 hour).

value: Spleen

value: Splenic B cells

value: Primary cells

value: WT

value: LPS priming (100 ng/mL), MSU (300 μg/mL)


title: B cell, LPS-primed, MSU-treated 1

description:
biol rep 1
NormCounts_B cell.txt
B cell_4-1


title: 06H026 [re-analysis]

description: reanalysis of GSM1636721

value: reverse


title: 06H021 [re-analysis]

description: reanalysis of GSM1636720


title: shHOXC6_2_1


title: shHOXC6_2_2


title: shHOXC6_1_3


title: 06H019 [re-analysis]

description: reanalysis of GSM1636719


title: cKO InfAmp 0.5 dpc

description: 100bp read length

value: oviduct

value: infundibulum and ampulla


title: B cell, LPS-primed 3

description:
biol rep 3
NormCounts_B cell.txt
B cell_3-3

value: LPS priming (100 ng/mL)


title: 06H014 [re-analysis]

description: reanalysis of GSM1636717


title: shHOXC6_1_2

value: RD-ES


title: 05H180 [re-analysis]

description: reanalysis of GSM1636714

value: Heparinised blood


title: 06H016 [re-analysis]

description: reanalysis of GSM1636718


title: 05H193 [re-analysis]

description: reanalysis of GSM1636715


title: B cell, LPS-primed 2

description:
biol rep 2
NormCounts_B cell.txt
B cell_3-2


title: 05H099 [re-analysis]

description: reanalysis of GSM1636713


title: shHOXC6_1_1

value: Ewing sarcoma


title: B cell, LPS-primed 1

description:
biol rep 1
NormCounts_B cell.txt
B cell_3-1


title: B cell, MSU-treated 2

description:
biol rep 2
NormCounts_B cell.txt
B cell_2-2

value: MSU (300 μg/mL)


title: 05H097 [re-analysis]

description: reanalysis of GSM1636712


title: NC_3


title: NC_1


title: 05H054 [re-analysis]

description: reanalysis of GSM1636708


title: 05H031 [re-analysis]

description: reanalysis of GSM1636706


title: 06H004 [re-analysis]

description: reanalysis of GSM1636716


title: B cell, MSU-treated 1

description:
biol rep 1
NormCounts_B cell.txt
B cell_2-1


title: B cell, Control 2

description:
biol rep 2
NormCounts_B cell.txt
B cell_1-3


title: 05H013 [re-analysis]

description: reanalysis of GSM1636705


title: 05H034 [re-analysis]

description: reanalysis of GSM1636707


title: ECAD_KO_3D_2

city: Nanjing

first: Yutong

last: Ge

state: Jiangsu

address: Changle Road 68

institute: Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38

source_name: CRC Line

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: CRC Line

value: colorectal cancer

value: ECAD KO


title: ECAD_KO_3D_3


title: B cell, Control 1

description:
biol rep 1
NormCounts_B cell.txt
B cell_1-2


title: 04H138 [re-analysis]

description: reanalysis of GSM1636704

value: Bone marrow

value: acute myeloid leukemia


title: 04H132 [re-analysis]

description: reanalysis of GSM1636702


title: ECAD_KO_3D_1


title: BMDC, LPS-primed, MSU-treated 2

description:
biol rep 2
NormCounts_BMDC.txt
DC4-2

value: Bone marrow-derived dendritic cells (BMDCs)


title: 04H135 [re-analysis]

description: reanalysis of GSM1636703


title: 04H127 [re-analysis]

description: reanalysis of GSM1636701


title: 05H090 [re-analysis]

description: reanalysis of GSM1636711


title: 04H120 [re-analysis]

description: reanalysis of GSM1636699


title: 05H065 [re-analysis]

description: reanalysis of GSM1636709


title: 05H072 [re-analysis]

description: reanalysis of GSM1636710


title: ECAD_KO_2D_3


title: NC_2


title: BMDC, LPS-primed, MSU-treated 3

description:
biol rep 3
NormCounts_BMDC.txt
DC4-3

value: Primary cells


title: 04H117 [re-analysis]

description: reanalysis of GSM1636697


title: 04H118 [re-analysis]

description: reanalysis of GSM1636698


title: ECAD_KO_2D_2


title: BMDC, LPS-primed, MSU-treated 1

description:
biol rep 1
NormCounts_BMDC.txt
DC4-1

value: WT


title: BMDC, LPS-primed 3

description:
biol rep 3
NormCounts_BMDC.txt
DC3-3


title: 04H123 [re-analysis]

description: reanalysis of GSM1636700


title: 04H111 [re-analysis]

description: reanalysis of GSM1636695


title: 04H103 [re-analysis]

description: reanalysis of GSM1636694


title: ECAD_KO_2D_1


title: 04H101 [re-analysis]

description: reanalysis of GSM1636693


title: Ctrl_3D_3

value: Ctrl


title: BMDC, LPS-primed 1

description:
biol rep 1
NormCounts_BMDC.txt
DC3-1


title: 04H068 [re-analysis]

description: reanalysis of GSM1636691

value: reverse


title: 04H096 [re-analysis]

description: reanalysis of GSM1636692


title: Ctrl_3D_2


title: Ctrl_3D_1


title: BMDC, LPS-primed 2

description:
biol rep 2
NormCounts_BMDC.txt
DC3-2


title: BMDC, MSU-treated 2

description:
biol rep 2
NormCounts_BMDC.txt
DC2-2


title: Ctrl_2D_3


title: 04H115 [re-analysis]

description: reanalysis of GSM1636696


title: BMDC, MSU-treated 1

description:
biol rep 1
NormCounts_BMDC.txt
DC2-1


title: 04H055 [re-analysis]

description: reanalysis of GSM1636690


title: 04H054 [re-analysis]

description: reanalysis of GSM1636689


title: BMDC, MSU-treated 3

description:
biol rep 3
NormCounts_BMDC.txt
DC2-3


title: 04H048 [re-analysis]

description: reanalysis of GSM1636688


title: 04H006 [re-analysis]

description: reanalysis of GSM1636685


title: 04H001 [re-analysis]

description: reanalysis of GSM1636684


title: Ctrl_2D_1


title: 04H017 [re-analysis]

description: reanalysis of GSM1636686


title: 03H094 [re-analysis]

description: reanalysis of GSM1636683


title: 04H039 [re-analysis]

description: reanalysis of GSM1636687


title: Ctrl_2D_2


title: 03H090 [re-analysis]

description: reanalysis of GSM1636682


title: BMDC, Control 3

description:
biol rep 3
NormCounts_BMDC.txt
DC1-3


title: Donor ascending 2

city: Palo Alto

first: Alex

last: Dalal

state: California

address: CT Surgery, 870 Quarry Rd Ext

department: Cardiothoracic Surgery

institute: Stanford University

description:
donor_asc_2
10x Genomics

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite 3.1.0’. Raw base-call files from NovaSeq 6000 sequencer were demultiplexed to first generate FASTQ files using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (GRCh38-3.0.0) genome, cell barcodes and unique molecular identifiers were filtered and corrected using thecellranger countpipeline (cellranger-6.1.2)
The final output filtered expression matrices were imported into the Seurat package in R and built into Seurat objects using the CreateSeuratObject function.
Standard quality control measures were then taken to exclude outliers representing doublets/clumps and free RNA. Cells with greater than 5% mitochondrial gene content were excluded Data normalization, scaling and regression by mitochondrial content were then performed using the SCTransform command in Seurat.
Integration using reciprocal principal component analysis (RPCA) based on highly conserved cell type markers across patients was then performed.
Assembly: GRCh38
Supplementary files format and content: Processed data files(.csv format) are exported expression matrices from the SCT assay within the Seurat package in R. Columns represent individual cell barcodes, rows represent features (genes) and numerical values represent the normalized expression data.

source_name: Ascending aorta

extract_protocol:
Fresh aortic root tissue was collected from the operating room within 30 minutes of excision and kept in cold HBSS (Sigma). Tissue was dissected to include all vascular layers and divided into four 50 mg pieces. Samples were then placed in digestion solution containing Liberase TM (10.4 U/mL working concentration, Roche) and elastase (8 U/mL, Sigma) and finely minced. Following 60 minutes of digestion at 37°C, digestates were filtered through a 70 μmol/L strainer, centrifuged and resuspended with fresh cold HBSS. Samples were sorted with FACS using Calcein green (ThermoFisher) for live/dead discrimination. Samples were immediately processed using a 10x Genomics microfluidics chip to generate barcoded Gel Bead-In Emulsions (GEMs) according to manufacturer protocols.
Individual sample libraries were generated from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

value: Ascending aorta

tag: Sex

value: Female

tag: age

value: 38 years

value: Donor


title: 03H081 [re-analysis]

description: reanalysis of GSM1636681


title: 03H070 [re-analysis]

description: reanalysis of GSM1636680


title: BMDC, Control 1

description:
biol rep 1
NormCounts_BMDC.txt
DC1-1


title: Donor root 2

description:
donor_root_2
10x Genomics

source_name: Aortic root

value: Aortic root


title: 03H036 [re-analysis]

description: reanalysis of GSM1636678


title: 03H060 [re-analysis]

description: reanalysis of GSM1636679


title: 03H030 [re-analysis]

description: reanalysis of GSM1636677

value: Heparinised blood


title: WT_7

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description:
0203_14
14_S14

data_processing:
FASTQ-file generation and demultiplexing was performed using bcl2fastq 4.0.3
Alignment to genome and gene counts were generated with the nfcore-rnaseq pipeline v. 3.11.2 using the STAR->Salmon workflow
Assembly: GRCm38
Supplementary files format and content: Tab-seperated file containing the raw gene counts for each sample. Rows specify genes by ENSEMBL_ID, and columns specify the sample

source_name: Skeletal muscle

extract_protocol:
Total RNA was isolated from QUAD with Trizol and RNeasy kit (Qiagen), and its quality was verified with 2100 Bioanalyzer Instrument (Agilent).
ssRNA-seq; Libraries were prepared using the Universal Plus mRNA-seq protocol (Tecan) as recommended by the manufacturer. Libraries were quantified with NuQuant using the Qubit fluorometer (Thermo Fisher Scientific), quality checked using a TapeStation instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina).

value: Skeletal muscle

tag: rin


title: Donor root 1

description:
donor_root_1
10x Genomics

value: Male

value: 39 years


title: 03H028 [re-analysis]

description: reanalysis of GSM1636676


title: LDS ascending 6

description:
LDS_asc_6
10x Genomics

value: 26 years


title: 02H046 [re-analysis]

description: reanalysis of GSM1636673

value: Bone marrow


title: LDS root 6

description:
LDS_root_6
10x Genomics


title: KO_7

description:
0203_13
13_S13

value: KO


title: 03H022 [re-analysis]

description: reanalysis of GSM1636674

value: acute myeloid leukemia


title: KO_8

description:
0203_15
15_S15


title: KO_6

description:
0203_11
11_S11


title: BMDC, Control 2

description:
biol rep 2
NormCounts_BMDC.txt
DC1-2

value: Bone marrow-derived dendritic cells (BMDCs)

value: Primary cells


title: 02H026 [re-analysis]

description: reanalysis of GSM1636670


title: Donor ascending 1

description:
donor_asc_1
10x Genomics


title: 03H024 [re-analysis]

description: reanalysis of GSM1636675


title: LDS root 5

description:
LDS_root_5
10x Genomics

value: 51 years


title: 01H002 [re-analysis]

description: reanalysis of GSM1636667

value: reverse


title: WT_5

description:
0203_10
10_S10

value: WT


title: WT_6

description:
0203_12
12_S12


title: 07H009 [re-analysis]

description: reanalysis of GSM1634300

extract_protocol:
TruSeq RNA Sample Preparation  (Illumina)
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
Sequencing libraries were prepared from total RNA using a poly-A selection and either the TruSeq unstranded RNA Sample Preparation (Illumina), TruSeq Stranded RNA Sample Preparation (Illumina) or the KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

value: unstranded


title: WT_8

description:
0203_16
16_S16


title: 02H043 [re-analysis]

description: reanalysis of GSM1636672


title: 02H025 [re-analysis]

description: reanalysis of GSM1636669


title: LDS ascending 4

description:
LDS_asc_4
10x Genomics

value: Ascending aorta

value: Female

value: 35 years


title: 02H033 [re-analysis]

description: reanalysis of GSM1636671


title: 02H003 [re-analysis]

description: reanalysis of GSM1636668

value: Heparinised blood


title: LDS ascending 5

description:
LDS_asc_5
10x Genomics


title: 06H146 [re-analysis]

description: reanalysis of GSM1634298


title: LDS root 4

description:
LDS_root_4
10x Genomics

value: Aortic root


title: KO_4

description:
0203_7
7_S7

value: Skeletal muscle


title: WT_4

description:
0203_8
8_S8


title: 06H011 [re-analysis]

description: reanalysis of GSM1634296


title: 05H195 [re-analysis]

description: reanalysis of GSM1634294


title: LDS ascending 2

description:
LDS_asc_2
10x Genomics

value: 29 years


title: LDS ascending 3

description:
LDS_asc_3
10x Genomics

value: Male

value: 36 years


title: 07H005 [re-analysis]

description: reanalysis of GSM1634299


title: LDS root 3

description:
LDS_root_3
10x Genomics


title: 06H010 [re-analysis]

description: reanalysis of GSM1634295

value: Bone marrow


title: LDS root 2

description:
LDS_root_2
10x Genomics


title: KO_3

description:
0203_5
5_S5

value: KO


title: WT_3

description:
0203_6
6_S6


title: 05H022 [re-analysis]

description: reanalysis of GSM1634288

value: acute myeloid leukemia


title: 05H186 [re-analysis]

description: reanalysis of GSM1634293


title: LDS ascending 1

description:
LDS_asc_1
10x Genomics

value: 48 years


title: 05H008 [re-analysis]

description: reanalysis of GSM1634287


title: 05H111 [re-analysis]

description: reanalysis of GSM1634291


title: 05H078 [re-analysis]

description: reanalysis of GSM1634290


title: KO_5

description:
0203_9
9_S9


title: LDS root 1

description:
LDS_root_1
10x Genomics


title: 04H108 [re-analysis]

description: reanalysis of GSM1634285