title: UGent11-60 Primed rep 1 lane 1


title: UGent11-2 Naive rep 3 lane 4

status: Public on Oct 13 2020

type: SRA

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

library_source: transcriptomic

data_processing:
Reads were trimmed using cutadapt versin 1.11 to remove the “QuantSeq FWD” adaptor sequence
The reads were mapped against the Mus musculus GRCm38.p5 reference genome using CLC genomics workbench version 9.0.1 (CLC)
Only the reads that didn’t map against the GRCm38.p5 genome were subsequently mapped against the Homo sapiens hg19 GRCH37.74 genome using CLC
Count tables were generated by counting the reads that mapped against the genes defined by the Ensembl GRCh37.74 gene transfer format file (GTF) and exported from CLC
Genome_build: Mus musculus GRCm38.p5
Genome_build: Homo sapiens hg19 GRCh37.74
Supplementary_files_format_and_content: comma separated values files including Gene counts, Gene ID and other gene information

molecule: total RNA

organism: Homo sapiens

source_name: Human embryonic stem cells

growth_protocol: Primed hESC lines, UGent11-2 (female XX) and UGent11-60 (female XX) were cultured on mitomycin-C-treated (MEFs) and refreshed daily with primed medium.

extract_protocol:
Total RNA was extracted from biological triplicates of UGent11-2 and UGent11-60 hESC lines cultured in primed, Wnt-i and naive conditions, using the RNeasy mini kit (Qiagen), including a DNase digestion step
500 ng of RNA was used for library preparation using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen) following the manufacturer's protocol.

treatment_protocol: Primed hESCs were converted to Wnt-i hESCs by refreshing daily with Wnt-i medium (see above) for 5 consecutive passages; and to naive hESCs by refreshing daily with naive medium for 5 consecutive passages.

tag: cell line

tag: cell type

value: hESC

tag: passage

tag: treatment

value: Naive


title: UGent11-2 Naive rep 3 lane 1


title: UGent11-2 Naive rep 3 lane 3


title: UGent11-2 Naive rep 1 lane 4


title: UGent11-60 Primed rep 1 lane 3

value: Primed


title: UGent11-2 Naive rep 2 lane 4


title: UGent11-60 Primed rep 1 lane 2


title: UGent11-2 Naive rep 2 lane 1


title: UGent11-60 Primed rep 3 lane 3


title: UGent11-2 Naive rep 1 lane 3


title: UGent11-2 Wnt-i rep 3 lane 3

value: Wnt-i


title: UGent11-2 Naive rep 1 lane 2


title: UGent11-2 Naive rep 1 lane 1


title: UGent11-2 Wnt-i rep 3 lane 4


title: UGent11-2 Wnt-i rep 3 lane 1


title: UGent11-2 Wnt-i rep 2 lane 3


title: UGent11-2 Wnt-i rep 2 lane 4


title: UGent11-2 Wnt-i rep 2 lane 2


title: UGent11-2 Wnt-i rep 3 lane 2


title: UGent11-2 Wnt-i rep 1 lane 3


title: UGent11-2 Wnt-i rep 2 lane 1


title: UGent11-2 Wnt-i rep 1 lane 4


title: UGent11-2 Wnt-i rep 1 lane 2


title: UGent11-2 Naive rep 2 lane 2


title: UGent11-2 Primed rep 3 lane 1


title: UGent11-2 Primed rep 2 lane 1


title: UGent11-2 Primed rep 2 lane 2


title: UGent11-2 Primed rep 2 lane 4


title: UGent11-2 Primed rep 3 lane 2


title: UGent11-2 Primed rep 2 lane 3


title: UGent11-2 Primed rep 1 lane 4


title: UGent11-2 Primed rep 1 lane 1


title: UGent11-2 Primed rep 1 lane 3


title: UGent11-2 Primed rep 3 lane 4


title: UGent11-2 Primed rep 1 lane 2


title: P9_L.EPSCs_SmartSeq2

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

institute: KU Leuven

data_processing:
Sequencing reads were mapped to mm10 reference genome using STAR 2.5.3a (Dobin et al., 2013). On average, 77,16% of reads were uniquely mapped and only those were kept for further analyses. Subsequently, the featureCounts function from the R Bioconductor package “Rsubread” (version 1.5.2) (Liao et al. 2019) was used to assign mapped reads to genomic features.
DESeq2 package and the associated protocol (Love et al. 2014) was used. Only genes that express at least 10 reads in total across all libraries were retained. PCA was performed using plotPCA function from the DESeq2 package with input of top 500 most variable genes after rlog transformation. Unless mentioned otherwise, gene expression was presented as log2 values after size-factor normalization for the differences in library size (DESeq2).
Smart-Seq2 read files (E2.5 and E4.5 embryos, and three pluripotent stem cell conditions: ESCs cultured in 2iLif, L-EPSCs, and D-EPSCs) were mapped to the mouse reference genome (mm10) using STAR aligner and only uniquely mapped reads were used for expression level estimation as reads per kilobase of gene model and million mappable reads (RPKMs) using RefSeq annotation.
Loom files were generated using export2loom function from pySCENIC package (0.9.15)
Genome_build: mm10
Supplementary_files_format_and_content: bulk_norm.csv
RPKM_matrix.txt
Loom files containing processed, normalized expression, regulon activity and clustering metadata, as well as UMAP embeddings.

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: L-EPSCs were cultured in a base media prepared as follows: DMEM/F12 (ThermoFisher Scientific 21331020); 20% KSR (ThermoFisher Scientific 10828028); 1x Glutamax (ThermoFisher Scientific 35050061) (or DMEM/F12 (Gibco, 13320074), 20% KnockOut Serum Replacement (KSR, Gibco, 10828028 ), 2.25 mM L-glutamine); 1x NEAA (ThermoFisher Scientific 11140-050); 0.1 mM β-mercaptoethanol (ThermoFisher Scientific 21985023 or Merck, M3148 SIGMA). This base media was supplemented with 10 ng/mL hLIF (Peprotech 300-05) or 1000 U/ml homemade mouse LIF; 1 µM PD0325901 (Tocris 4192 or Axon 1408); 3 µM CHIR99021 (Tocris 4423, or Axon 1386); 4 µM TCS JNK 60 (Tocris 3222); 5 µM XAV939 (Sigma-Aldrich X3004); 10 µM SB203580 (Tocris 1402); and 0.3 µM A-419259 (Santa Cruz sc-36109; or Tocris 39142). L-EPSCs were cultured at 20% O2 and 5% CO2 at 37°C on MMC-inactivated SNL76/7 feeder cells or MMC-inactivated MEF feeders (approx 50-80,000 cells/cm2). SNL feeders were plated on 0.2% gelatin-coated plates in ES base media (described above). SNL plates were used within 3-4 days and washed with DPBS prior to plating L-EPSCs. Media was changed daily, with single-cell passaging every 3 days using accutase at split ratios between 1:3 and 1:12.

extract_protocol:
Total RNA was isolated from 2iLif ESCs and L-EPSCs reprogramming intermediates at indicated days using TRIzol reagent according to manufacturer’s protocol.
4 µg of total RNA was used to generate libraries using of stranded poly(A) mRNA-Seq library with the KAPA stranded mRNA Library prep kit (KAPA Biosystems, KK8421). Libraries concentration was quantified with Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Q32854), and the final pool was generated by combining individual libraries in equimolar ratio. Libraries were sequenced on an Illumina HiSeq 4000 instrument (Illumina) with 51 bp reads and read depth ranging ~33 mln reads.
Single-cells from stem cells were sorted by FACS into 384 well plates containing lysis and RT, whereas embryo cells were manually picked and directly dispensed into lysis buffer containing RT. The current study generated cDNA libraries using the Smart-seq2 protocol.

treatment_protocol: Mouse ESCs grown in 2i/LIF are switched to L-EPSC medium and total RNA was collected at day (D) 0, D3, D5, D7, D9, D11, D13 and D15.

value: embryonic stem cells

tag: culture conditions


title: P7_L.EPSCs_SmartSeq2


title: P8_L.EPSCs_SmartSeq2


title: P5_L.EPSCs_SmartSeq2


title: P6_L.EPSCs_SmartSeq2


title: UGent11-2 Wnt-i rep 1 lane 1


title: P4_L.EPSCs_SmartSeq2


title: P11_L.EPSCs_SmartSeq2


title: P3_L.EPSCs_SmartSeq2


title: UGent11-2 Primed rep 3 lane 3


title: P2_L.EPSCs_SmartSeq2


title: P10_L.EPSCs_SmartSeq2


title: P1_L.EPSCs_SmartSeq2


title: O9_L.EPSCs_SmartSeq2


title: O7_L.EPSCs_SmartSeq2


title: O8_L.EPSCs_SmartSeq2


title: O6_L.EPSCs_SmartSeq2


title: O5_L.EPSCs_SmartSeq2


title: O3_L.EPSCs_SmartSeq2


title: O4_L.EPSCs_SmartSeq2


title: O2_L.EPSCs_SmartSeq2


title: O11_L.EPSCs_SmartSeq2


title: O10_L.EPSCs_SmartSeq2


title: O1_L.EPSCs_SmartSeq2


title: O12_L.EPSCs_SmartSeq2


title: N8_L.EPSCs_SmartSeq2


title: N9_L.EPSCs_SmartSeq2


title: N6_L.EPSCs_SmartSeq2


title: N7_L.EPSCs_SmartSeq2


title: N3_L.EPSCs_SmartSeq2


title: N5_L.EPSCs_SmartSeq2


title: N4_L.EPSCs_SmartSeq2


title: N12_L.EPSCs_SmartSeq2


title: N11_L.EPSCs_SmartSeq2


title: N10_L.EPSCs_SmartSeq2


title: N2_L.EPSCs_SmartSeq2


title: M7_L.EPSCs_SmartSeq2


title: M8_L.EPSCs_SmartSeq2


title: M6_L.EPSCs_SmartSeq2


title: N1_L.EPSCs_SmartSeq2


title: M5_L.EPSCs_SmartSeq2


title: M4_L.EPSCs_SmartSeq2


title: M3_L.EPSCs_SmartSeq2


title: M11_L.EPSCs_SmartSeq2


title: M12_L.EPSCs_SmartSeq2


title: M2_L.EPSCs_SmartSeq2


title: M1_L.EPSCs_SmartSeq2


title: M10_L.EPSCs_SmartSeq2


title: TL194_SHEP_MYCN_T58A_DMSO_3

city: Houston

first: Tong

last: Liang

state: TX

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

description: RNA-seq in DMSO SHEP_MYCN_T58A rep3

data_processing:
Sequenced reads were aligned to HG19 referenece genome using HISAT
FPKM were caluclated by cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: text file with fpkm

source_name: Neuroblastoma

growth_protocol:
10% FBS, DMEM
SH-EP-MYCN cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS.

extract_protocol:
Direct-zol RNA Miniprep Kits (R2050; Zymo Scientific)
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: CYC065 drug treatment was performed by addition of 1uM CYC065 to growth media for 6hrs

value: SHEP MYCN

value: Neuroblastoma

tag: exogenous myc genotype

value: DMSO for 6HR

tag: barcode

value: ATGTCAGA


title: L7_L.EPSCs_SmartSeq2


title: L6_L.EPSCs_SmartSeq2


title: L9_L.EPSCs_SmartSeq2


title: L5_L.EPSCs_SmartSeq2


title: M9_L.EPSCs_SmartSeq2


title: L2_L.EPSCs_SmartSeq2


title: L4_L.EPSCs_SmartSeq2


title: L12_L.EPSCs_SmartSeq2


title: L11_L.EPSCs_SmartSeq2


title: K8_L.EPSCs_SmartSeq2


title: L10_L.EPSCs_SmartSeq2


title: K9_L.EPSCs_SmartSeq2


title: K7_L.EPSCs_SmartSeq2


title: L1_L.EPSCs_SmartSeq2


title: K5_L.EPSCs_SmartSeq2


title: K4_L.EPSCs_SmartSeq2


title: L3_L.EPSCs_SmartSeq2


title: K2_L.EPSCs_SmartSeq2


title: K10_L.EPSCs_SmartSeq2


title: J9_L.EPSCs_SmartSeq2


title: K11_L.EPSCs_SmartSeq2


title: J6_L.EPSCs_SmartSeq2


title: K12_L.EPSCs_SmartSeq2


title: J8_L.EPSCs_SmartSeq2


title: K1_L.EPSCs_SmartSeq2


title: J7_L.EPSCs_SmartSeq2


title: TL185_SHEP_MYCN_WT_CYC065_3

description: RNA-seq in CYC065 SHEP_MYCN_WT rep3

value: WT

value: 1uM CYC065 for 6HR

value: GCCAATAT


title: J5_L.EPSCs_SmartSeq2


title: J4_L.EPSCs_SmartSeq2


title: J3_L.EPSCs_SmartSeq2


title: J12_L.EPSCs_SmartSeq2


title: J11_L.EPSCs_SmartSeq2


title: J2_L.EPSCs_SmartSeq2


title: J10_L.EPSCs_SmartSeq2


title: I3_L.EPSCs_SmartSeq2


title: I2_L.EPSCs_SmartSeq2


title: I10_L.EPSCs_SmartSeq2


title: J1_L.EPSCs_SmartSeq2


title: I1_L.EPSCs_SmartSeq2


title: I11_L.EPSCs_SmartSeq2


title: I12_L.EPSCs_SmartSeq2


title: H8_L.EPSCs_SmartSeq2


title: H6_L.EPSCs_SmartSeq2


title: H7_L.EPSCs_SmartSeq2


title: H5_L.EPSCs_SmartSeq2


title: H4_L.EPSCs_SmartSeq2


title: H2_L.EPSCs_SmartSeq2


title: H3_L.EPSCs_SmartSeq2


title: H1_L.EPSCs_SmartSeq2


title: G8_L.EPSCs_SmartSeq2


title: G9_L.EPSCs_SmartSeq2


title: H9_L.EPSCs_SmartSeq2


title: H11_L.EPSCs_SmartSeq2


title: G5_L.EPSCs_SmartSeq2


title: G7_L.EPSCs_SmartSeq2


title: G6_L.EPSCs_SmartSeq2


title: G3_L.EPSCs_SmartSeq2


title: G4_L.EPSCs_SmartSeq2


title: G2_L.EPSCs_SmartSeq2


title: G12_L.EPSCs_SmartSeq2


title: G10_L.EPSCs_SmartSeq2


title: F9_L.EPSCs_SmartSeq2


title: F8_L.EPSCs_SmartSeq2


title: UGent11-2 Naive rep 2 lane 3


title: H12_L.EPSCs_SmartSeq2


title: F4_L.EPSCs_SmartSeq2


title: F5_L.EPSCs_SmartSeq2


title: G11_L.EPSCs_SmartSeq2


title: F3_L.EPSCs_SmartSeq2


title: F2_L.EPSCs_SmartSeq2


title: H10_L.EPSCs_SmartSeq2


title: F12_L.EPSCs_SmartSeq2


title: K6_L.EPSCs_SmartSeq2


title: F10_L.EPSCs_SmartSeq2


title: E9_L.EPSCs_SmartSeq2


title: F11_L.EPSCs_SmartSeq2


title: F1_L.EPSCs_SmartSeq2


title: E8_L.EPSCs_SmartSeq2


title: G1_L.EPSCs_SmartSeq2


title: E4_L.EPSCs_SmartSeq2


title: E2_L.EPSCs_SmartSeq2


title: E6_L.EPSCs_SmartSeq2


title: E1_L.EPSCs_SmartSeq2


title: E7_L.EPSCs_SmartSeq2


title: E10_L.EPSCs_SmartSeq2


title: F6_L.EPSCs_SmartSeq2


title: E3_L.EPSCs_SmartSeq2


title: E5_L.EPSCs_SmartSeq2


title: E11_L.EPSCs_SmartSeq2


title: D8_L.EPSCs_SmartSeq2


title: D7_L.EPSCs_SmartSeq2


title: D9_L.EPSCs_SmartSeq2


title: D6_L.EPSCs_SmartSeq2


title: D5_L.EPSCs_SmartSeq2


title: D4_L.EPSCs_SmartSeq2


title: D3_L.EPSCs_SmartSeq2


title: D11_L.EPSCs_SmartSeq2


title: D10_L.EPSCs_SmartSeq2


title: C8_L.EPSCs_SmartSeq2


title: C6_L.EPSCs_SmartSeq2


title: C7_L.EPSCs_SmartSeq2


title: C3_L.EPSCs_SmartSeq2


title: C4_L.EPSCs_SmartSeq2


title: C12_L.EPSCs_SmartSeq2


title: C2_L.EPSCs_SmartSeq2


title: C11_L.EPSCs_SmartSeq2


title: B8_L.EPSCs_SmartSeq2


title: C10_L.EPSCs_SmartSeq2


title: B5_L.EPSCs_SmartSeq2


title: B4_L.EPSCs_SmartSeq2


title: B3_L.EPSCs_SmartSeq2


title: B11_L.EPSCs_SmartSeq2


title: B12_L.EPSCs_SmartSeq2


title: D2_L.EPSCs_SmartSeq2


title: B6_L.EPSCs_SmartSeq2


title: B1_L.EPSCs_SmartSeq2


title: A9_L.EPSCs_SmartSeq2


title: D12_L.EPSCs_SmartSeq2


title: A8_L.EPSCs_SmartSeq2


title: C9_L.EPSCs_SmartSeq2


title: A7_L.EPSCs_SmartSeq2


title: C5_L.EPSCs_SmartSeq2


title: C1_L.EPSCs_SmartSeq2


title: A5_L.EPSCs_SmartSeq2


title: A3_L.EPSCs_SmartSeq2


title: B9_L.EPSCs_SmartSeq2


title: A4_L.EPSCs_SmartSeq2


title: A12_L.EPSCs_SmartSeq2


title: A1_L.EPSCs_SmartSeq2


title: A11_L.EPSCs_SmartSeq2


title: P23_D.EPSCs_SmartSeq2


title: P5_2i_SmartSeq2


title: P4_2i_SmartSeq2


title: P8_2i_SmartSeq2


title: B7_L.EPSCs_SmartSeq2


title: B10_L.EPSCs_SmartSeq2


title: P6_2i_SmartSeq2


title: P19_D.EPSCs_SmartSeq2


title: P17_D.EPSCs_SmartSeq2


title: P3_2i_SmartSeq2


title: P22_D.EPSCs_SmartSeq2


title: P7_2i_SmartSeq2


title: P18_D.EPSCs_SmartSeq2


title: P15_D.EPSCs_SmartSeq2


title: P2_2i_SmartSeq2


title: P16_D.EPSCs_SmartSeq2


title: A6_L.EPSCs_SmartSeq2


title: A10_L.EPSCs_SmartSeq2


title: P14_D.EPSCs_SmartSeq2


title: P13_D.EPSCs_SmartSeq2


title: O9_2i_SmartSeq2


title: O8_2i_SmartSeq2


title: P10_2i_SmartSeq2


title: O7_2i_SmartSeq2


title: P1_2i_SmartSeq2


title: P20_D.EPSCs_SmartSeq2


title: O22_D.EPSCs_SmartSeq2


title: O4_2i_SmartSeq2


title: O3_2i_SmartSeq2


title: O24_D.EPSCs_SmartSeq2


title: O23_D.EPSCs_SmartSeq2


title: O2_2i_SmartSeq2


title: O20_D.EPSCs_SmartSeq2


title: O19_D.EPSCs_SmartSeq2


title: O17_D.EPSCs_SmartSeq2


title: O18_D.EPSCs_SmartSeq2


title: P11_2i_SmartSeq2


title: O15_D.EPSCs_SmartSeq2


title: O16_D.EPSCs_SmartSeq2


title: O14_D.EPSCs_SmartSeq2


title: O13_D.EPSCs_SmartSeq2


title: O11_2i_SmartSeq2


title: O12_2i_SmartSeq2


title: O1_2i_SmartSeq2


title: O10_2i_SmartSeq2


title: K3_L.EPSCs_SmartSeq2


title: O6_2i_SmartSeq2


title: N7_2i_SmartSeq2


title: N6_2i_SmartSeq2


title: N8_2i_SmartSeq2


title: N4_2i_SmartSeq2


title: O5_2i_SmartSeq2


title: N5_2i_SmartSeq2


title: O21_D.EPSCs_SmartSeq2


title: N22_D.EPSCs_SmartSeq2


title: N21_D.EPSCs_SmartSeq2


title: N3_2i_SmartSeq2


title: N20_D.EPSCs_SmartSeq2


title: N23_D.EPSCs_SmartSeq2


title: N18_D.EPSCs_SmartSeq2


title: N19_D.EPSCs_SmartSeq2


title: N16_D.EPSCs_SmartSeq2


title: N13_D.EPSCs_SmartSeq2


title: N17_D.EPSCs_SmartSeq2


title: N11_2i_SmartSeq2


title: N10_2i_SmartSeq2


title: N15_D.EPSCs_SmartSeq2


title: N14_D.EPSCs_SmartSeq2


title: N9_2i_SmartSeq2


title: N12_2i_SmartSeq2


title: N1_2i_SmartSeq2


title: M9_2i_SmartSeq2


title: M8_2i_SmartSeq2


title: M7_2i_SmartSeq2


title: M5_2i_SmartSeq2


title: M6_2i_SmartSeq2


title: M3_2i_SmartSeq2


title: N24_D.EPSCs_SmartSeq2


title: M24_D.EPSCs_SmartSeq2


title: M23_D.EPSCs_SmartSeq2


title: M4_2i_SmartSeq2


title: M22_D.EPSCs_SmartSeq2


title: N2_2i_SmartSeq2


title: M21_D.EPSCs_SmartSeq2


title: M20_D.EPSCs_SmartSeq2


title: M2_2i_SmartSeq2


title: M15_D.EPSCs_SmartSeq2


title: M19_D.EPSCs_SmartSeq2


title: M17_D.EPSCs_SmartSeq2


title: M16_D.EPSCs_SmartSeq2


title: L9_2i_SmartSeq2


title: M13_D.EPSCs_SmartSeq2


title: M12_2i_SmartSeq2


title: M11_2i_SmartSeq2


title: L6_2i_SmartSeq2


title: M1_2i_SmartSeq2


title: L24_D.EPSCs_SmartSeq2


title: M10_2i_SmartSeq2


title: L23_D.EPSCs_SmartSeq2


title: L3_2i_SmartSeq2


title: L7_2i_SmartSeq2


title: L5_2i_SmartSeq2


title: L21_D.EPSCs_SmartSeq2


title: L2_2i_SmartSeq2


title: L22_D.EPSCs_SmartSeq2


title: L4_2i_SmartSeq2


title: L20_D.EPSCs_SmartSeq2


title: L17_D.EPSCs_SmartSeq2


title: L19_D.EPSCs_SmartSeq2


title: L18_D.EPSCs_SmartSeq2


title: F7_L.EPSCs_SmartSeq2


title: M14_D.EPSCs_SmartSeq2


title: M18_D.EPSCs_SmartSeq2


title: L15_D.EPSCs_SmartSeq2


title: L14_D.EPSCs_SmartSeq2


title: L13_D.EPSCs_SmartSeq2


title: L11_2i_SmartSeq2


title: L1_2i_SmartSeq2


title: L10_2i_SmartSeq2


title: K9_2i_SmartSeq2


title: K8_2i_SmartSeq2


title: K7_2i_SmartSeq2


title: K6_2i_SmartSeq2


title: K5_2i_SmartSeq2


title: K24_D.EPSCs_SmartSeq2


title: L8_2i_SmartSeq2


title: K23_D.EPSCs_SmartSeq2


title: K3_2i_SmartSeq2


title: K22_D.EPSCs_SmartSeq2


title: L16_D.EPSCs_SmartSeq2


title: K20_D.EPSCs_SmartSeq2


title: K21_D.EPSCs_SmartSeq2


title: K19_D.EPSCs_SmartSeq2


title: K18_D.EPSCs_SmartSeq2


title: K2_2i_SmartSeq2


title: K16_D.EPSCs_SmartSeq2


title: K15_D.EPSCs_SmartSeq2


title: K13_D.EPSCs_SmartSeq2


title: K17_D.EPSCs_SmartSeq2


title: K12_2i_SmartSeq2


title: L12_2i_SmartSeq2


title: K10_2i_SmartSeq2


title: K11_2i_SmartSeq2


title: K1_2i_SmartSeq2


title: J9_2i_SmartSeq2


title: J8_2i_SmartSeq2


title: J6_2i_SmartSeq2


title: J7_2i_SmartSeq2


title: K4_2i_SmartSeq2


title: J4_2i_SmartSeq2


title: J5_2i_SmartSeq2


title: J3_2i_SmartSeq2


title: J21_D.EPSCs_SmartSeq2


title: J24_D.EPSCs_SmartSeq2


title: J19_D.EPSCs_SmartSeq2


title: J20_D.EPSCs_SmartSeq2


title: J17_D.EPSCs_SmartSeq2


title: J18_D.EPSCs_SmartSeq2


title: K14_D.EPSCs_SmartSeq2


title: J16_D.EPSCs_SmartSeq2


title: J2_2i_SmartSeq2


title: J15_D.EPSCs_SmartSeq2


title: J13_D.EPSCs_SmartSeq2


title: J14_D.EPSCs_SmartSeq2


title: J12_2i_SmartSeq2


title: J11_2i_SmartSeq2


title: J1_2i_SmartSeq2


title: I9_2i_SmartSeq2


title: J10_2i_SmartSeq2


title: I8_2i_SmartSeq2


title: I7_2i_SmartSeq2


title: I5_2i_SmartSeq2


title: I6_2i_SmartSeq2


title: I4_2i_SmartSeq2


title: I24_D.EPSCs_SmartSeq2


title: I23_D.EPSCs_SmartSeq2


title: I22_D.EPSCs_SmartSeq2


title: J23_D.EPSCs_SmartSeq2


title: I3_2i_SmartSeq2


title: I21_D.EPSCs_SmartSeq2


title: I20_D.EPSCs_SmartSeq2


title: I19_D.EPSCs_SmartSeq2


title: I2_2i_SmartSeq2


title: I17_D.EPSCs_SmartSeq2


title: I18_D.EPSCs_SmartSeq2


title: I16_D.EPSCs_SmartSeq2


title: I12_2i_SmartSeq2


title: I11_2i_SmartSeq2


title: I13_D.EPSCs_SmartSeq2


title: I14_D.EPSCs_SmartSeq2


title: I15_D.EPSCs_SmartSeq2


title: I10_2i_SmartSeq2


title: H9_2i_SmartSeq2


title: H8_2i_SmartSeq2


title: I1_2i_SmartSeq2


title: H6_2i_SmartSeq2


title: H7_2i_SmartSeq2


title: H5_2i_SmartSeq2


title: H3_2i_SmartSeq2


title: H24_D.EPSCs_SmartSeq2


title: H4_2i_SmartSeq2


title: H21_D.EPSCs_SmartSeq2


title: H22_D.EPSCs_SmartSeq2


title: H23_D.EPSCs_SmartSeq2


title: H2_2i_SmartSeq2


title: H19_D.EPSCs_SmartSeq2


title: H20_D.EPSCs_SmartSeq2


title: H18_D.EPSCs_SmartSeq2


title: H17_D.EPSCs_SmartSeq2


title: H16_D.EPSCs_SmartSeq2


title: H15_D.EPSCs_SmartSeq2


title: H13_D.EPSCs_SmartSeq2


title: H14_D.EPSCs_SmartSeq2


title: H11_2i_SmartSeq2


title: H10_2i_SmartSeq2


title: H12_2i_SmartSeq2


title: H1_2i_SmartSeq2


title: G8_2i_SmartSeq2


title: G7_2i_SmartSeq2


title: G5_2i_SmartSeq2


title: G9_2i_SmartSeq2


title: G3_2i_SmartSeq2


title: G4_2i_SmartSeq2


title: G22_D.EPSCs_SmartSeq2


title: G23_D.EPSCs_SmartSeq2


title: G21_D.EPSCs_SmartSeq2


title: G24_D.EPSCs_SmartSeq2


title: G19_D.EPSCs_SmartSeq2


title: G17_D.EPSCs_SmartSeq2


title: G2_2i_SmartSeq2


title: G13_D.EPSCs_SmartSeq2


title: G20_D.EPSCs_SmartSeq2


title: G15_D.EPSCs_SmartSeq2


title: G14_D.EPSCs_SmartSeq2


title: G6_2i_SmartSeq2


title: F24_D.EPSCs_SmartSeq2


title: F22_D.EPSCs_SmartSeq2


title: F23_D.EPSCs_SmartSeq2


title: F20_D.EPSCs_SmartSeq2


title: F21_D.EPSCs_SmartSeq2


title: G10_2i_SmartSeq2


title: G12_2i_SmartSeq2


title: F2_2i_SmartSeq2


title: G18_D.EPSCs_SmartSeq2


title: G11_2i_SmartSeq2


title: F8_2i_SmartSeq2


title: F9_2i_SmartSeq2


title: F3_2i_SmartSeq2


title: F18_D.EPSCs_SmartSeq2


title: F6_2i_SmartSeq2


title: F4_2i_SmartSeq2


title: F5_2i_SmartSeq2


title: G1_2i_SmartSeq2


title: G16_D.EPSCs_SmartSeq2


title: F17_D.EPSCs_SmartSeq2


title: F16_D.EPSCs_SmartSeq2


title: F15_D.EPSCs_SmartSeq2


title: F13_D.EPSCs_SmartSeq2


title: F14_D.EPSCs_SmartSeq2


title: F10_2i_SmartSeq2


title: F11_2i_SmartSeq2


title: F12_2i_SmartSeq2


title: F7_2i_SmartSeq2


title: F1_2i_SmartSeq2


title: E9_2i_SmartSeq2


title: E7_2i_SmartSeq2


title: E8_2i_SmartSeq2


title: F19_D.EPSCs_SmartSeq2


title: E5_2i_SmartSeq2


title: E6_2i_SmartSeq2


title: E24_D.EPSCs_SmartSeq2


title: E15_D.EPSCs_SmartSeq2


title: E23_2i_SmartSeq2


title: E14_D.EPSCs_SmartSeq2


title: E19_D.EPSCs_SmartSeq2


title: E21_D.EPSCs_SmartSeq2


title: E22_D.EPSCs_SmartSeq2


title: E18_D.EPSCs_SmartSeq2


title: E2_2i_SmartSeq2


title: E3_2i_SmartSeq2


title: E4_2i_SmartSeq2


title: E16_D.EPSCs_SmartSeq2


title: E12_2i_SmartSeq2


title: E11_2i_SmartSeq2


title: E17_D.EPSCs_SmartSeq2


title: E10_2i_SmartSeq2


title: E20_D.EPSCs_SmartSeq2


title: E13_D.EPSCs_SmartSeq2


title: E1_2i_SmartSeq2


title: D9_2i_SmartSeq2


title: D8_2i_SmartSeq2


title: P14

type: RNA

city: Barcelona

first: Joan

last: Seoane

address: Vall d'Hebron 119-129

country: Spain

institute: VHIO

hyb_protocol: nCounter XT CodeSet Gene Expression Assays protocol using the nCounter PanCancer Immune Profiling Panel, NanoString

scan_protocol: nCounter MAX Analysis System, NanoString

data_processing: nSolver Analysis Software, NanoString

source_name: Brain metastasis

label_protocol: not provided

extract_protocol: RNeasy Mini Kit, Qiagen (fresh-frozen samples)

tag: tissue

value: Brain metastasis tumor

tag: cancer type

tag: run date


title: P15


title: P16


title: P12_2


title: P13


title: P19


title: P9_2


title: P11_2


title: D24_D.EPSCs_SmartSeq2


title: D2_2i_SmartSeq2


title: D22_D.EPSCs_SmartSeq2


title: D4_2i_SmartSeq2


title: D6_2i_SmartSeq2


title: P17


title: D7_2i_SmartSeq2


title: P50


title: D21_D.EPSCs_SmartSeq2


title: P10


title: P7_2


title: P18


title: P47


title: D20_D.EPSCs_SmartSeq2


title: D5_2i_SmartSeq2


title: D3_2i_SmartSeq2


title: D23_D.EPSCs_SmartSeq2


title: D19_D.EPSCs_SmartSeq2


title: P6_2


title: P46


title: P8


title: D18_D.EPSCs_SmartSeq2


title: D16_D.EPSCs_SmartSeq2


title: D15_D.EPSCs_SmartSeq2


title: D14_D.EPSCs_SmartSeq2


title: P4


title: P49


title: P48


title: P3_2


title: D17_D.EPSCs_SmartSeq2


title: P2


title: C8_2i_SmartSeq2


title: C7_2i_SmartSeq2


title: D10_2i_SmartSeq2


title: D12_2i_SmartSeq2


title: D11_2i_SmartSeq2


title: C9_2i_SmartSeq2


title: P38


title: P42


title: P37


title: P44


title: P1_2


title: D13_D.EPSCs_SmartSeq2


title: P41


title: P35


title: P40


title: P39


title: P34


title: C4_2i_SmartSeq2


title: C24_D.EPSCs_SmartSeq2


title: C6_2i_SmartSeq2


title: C5_2i_SmartSeq2


title: C3_2i_SmartSeq2


title: C22_D.EPSCs_SmartSeq2


title: C23_D.EPSCs_SmartSeq2


title: C21_D.EPSCs_SmartSeq2


title: C2_2i_SmartSeq2


title: P36


title: C18_D.EPSCs_SmartSeq2


title: C17_D.EPSCs_SmartSeq2


title: C19_D.EPSCs_SmartSeq2


title: C16_D.EPSCs_SmartSeq2


title: C14_D.EPSCs_SmartSeq2


title: P5


title: P43


title: P31


title: P45


title: P30


title: P33


title: P29


title: P25


title: P26


title: P24


title: P22


title: P28


title: P27


title: B9_2i_SmartSeq2


title: C13_D.EPSCs_SmartSeq2


title: P12


title: C12_2i_SmartSeq2


title: C11_2i_SmartSeq2


title: C10_2i_SmartSeq2


title: P21


title: P23


title: C1_2i_SmartSeq2


title: C15_D.EPSCs_SmartSeq2


title: P7


title: P6


title: P9


title: B7_2i_SmartSeq2


title: B8_2i_SmartSeq2


title: P11


title: B3_2i_SmartSeq2


title: B5_2i_SmartSeq2


title: B4_2i_SmartSeq2


title: P3


title: PPF.P30.E

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

department: Surgery

institute: Stanford University

data_processing:
scRNA seq: Data was log-normalized and evaluated using uniform manifold approximation and projection (UMAP) analysis in Seurat (v3.2),(Becht et al., 2019) which identified six distinct transcriptionally-defined subpopulations, agnostic to lineage (PPF vs PNF) or wounded state (unwounded vs healed wound [POD 14]) within the mouse ventral dermis. Automated cell annotation profiling using SingleR (v3.11) against two murine reference sets identified each independent subpopulation as overwhelmingly ‘fibroblast’ in character.
scRNA-seq: Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 1000 transcripts profiled and less than 10% of their transcriptome of mitochondrial origin.
scRNA-seq: UMIs from each cell barcode were retained for all downstream analysis. Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
scRNA-seq: Hashtag oligos (HTOs) for mouse samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a ‘negative’ HTO distribution is calculated. For each HTO,  the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Cells that are positive for more than one HTOs are annotated as doublets and removed. Cells that are not positive for any HTO are also removed.  The 8 mouse samples were represented in the two samples by the following hashtag antibodies:                                                                                Tube 1:   1) Rostral POD-14 Wound: TotalSeq-BO301 antimouse hashtag 1 antibody  2) PNF Rostral POD-14 Wound:TotalSeq-BO302 antimouse hashtag 2 antibody  3) PPF Rostral UnWounded:TotalSeq-BO304 antimouse hashtag 4 antibody  4) PPF Rostral UnWounded:TotalSeq-BO305 antimouse hashtag 5 antibody Tube 2 :  5) PPF Caudal POD-14 Wound: TotalSeq-BO301 antimouse hashtag 1 antibody  6) PNF Caudal POD-14 Wound:TotalSeq-BO302 antimouse hashtag 2 antibody  7) PPF Caudal UnWounded:TotalSeq-BO304 antimouse hashtag 4 antibody  8) PPF Caudal UnWounded:TotalSeq-BO305 antimouse hashtag 5 antibody
scRNA-seq: As recommended [41], a threshold of P-adjusted < 0.1 was used to define significance for differentially expressed genes
Genome_build: scRNA-seq:  mm10 v3.0.0 for mouse
Supplementary_files_format_and_content: Filtered 10X matrix counts

source_name: Ventrum Skin.

extract_protocol:
RNA-seq and scRNA-seq: For mouse fibroblasts, fibroblasts were isolated from fresh specimens using FACS. RNA extraction was performed using Qiagen miRNeasy kit (cat. 1071023) with on column DAnase treatment per the manufacturer’s recommendations. The Clontech Smarter Ultra Low Input RNA kit (Takara Bio, Cat. 634848) was used to generate cDNA from 150 pg total RNA following the manufacturer’s recommendations.  Amplified cDNA was purified using SPRI Ampure Beads (Beckman Coulter, Cat. A63880) and the quality and quantity was measured using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA-seq: The Smarter Ultra Low Input RNA kit, from TakaraBio formerly Clontech (Catalog# 634848) was used to generate cDNA from total RNA using the standard protocol.  Amplified cDNA was purified using SPRI Ampure Beads from Beckman Coulter (Catalog # A63880). The quality and quantity was assed using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer.  Illumina Nextra-XT kit (Catalog #FC-131-1024) was used to generate libraries from 150pg of amplified cDNA following standard protocol.  Equal nanomole of uniquely indexed libraries was pooled and sequenced on HighSeq4000. (2X75 pair-end). scRNA-seq: cDNA was sheared to an average length of 300 basepairs using a Covaris S2 ultrasonicator (Covaris) and libraries were generated with the Clontech Low Input Library Prep kit (Takara Bio, Cat. 634947).  scRNA-seq libraries were prepared using the 10x Genomics Chromium platform.
scRNA-seq: The samples were uniquely barcoded, pooled, and sequenced onto two lanes of the NextSeq 500 (Illumina). A total of 300 million paired-end, 151 base pair reads were obtained, resulting in 50 million reads per sample.

treatment_protocol: Skin tissue from mouse specimens was minced on ice. The tissue was then digested for 60 minutes in a 37 deg C water bath agitator in 2 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4 deg C, resuspended in quench media, and filtered through 100, 70, and 40m cell strainers (Falcon cell strainer, ThermoFisher).

tag: strain

value: Prrx-Cre

value: Postnatal ventral skin

tag: genotype

value: Invoved in early limb bud mesenchyme and in a subset of craniofacial mesenchyme.

value: Fibroblasts


title: PPF.P30.D


title: PPF.P30.F


title: PPF.P30.C


title: P1


title: B24_D.EPSCs_SmartSeq2


title: PPF.P30.0.B


title: PPF.P30.0.A


title: B23_D.EPSCs_SmartSeq2


title: B22_L.EPSCs_SmartSeq2


title: B20_D.EPSCs_SmartSeq2


title: B2_2i_SmartSeq2


title: B6_2i_SmartSeq2


title: PPF.P1.A


title: PNF.P30.A


title: B21_D.EPSCs_SmartSeq2


title: B17_D.EPSCs_SmartSeq2


title: B19_D.EPSCs_SmartSeq2


title: PNF.P1.D


title: B18_D.EPSCs_SmartSeq2


title: PNF.P1.C


title: B16_D.EPSCs_SmartSeq2


title: B15_D.EPSCs_SmartSeq2


title: B14_D.EPSCs_SmartSeq2


title: PNF.P1.0.A


title: PPF.E18.5.B

value: Embryo ventral skin.


title: PPF.E18.5.A


title: PPF.P1.B


title: B12_2i_SmartSeq2


title: B11_2i_SmartSeq2


title: B13_D.EPSCs_SmartSeq2


title: PNF.P30.B


title: PNF_E18.5.D


title: PNF.P1.0.B


title: PNF_E18.5.A


title: B1_2i_SmartSeq2


title: PNF_E18.5.B


title: B10_2i_SmartSeq2


title: PPF.E16.5.B


title: PPF.E16.5.A


title: A6_2i_SmartSeq2


title: A7_2i_SmartSeq2


title: A8_2i_SmartSeq2


title: PNF.E16.5.A


title: PNF.E16.5.B


title: A4_2i_SmartSeq2


title: A5_2i_SmartSeq2


title: A3_2i_SmartSeq2


title: ChIP_Erkdko_ectopicJarid2_serum_input

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

description: serum medium

library_source: genomic

data_processing:
For the ChIP-Seq data analysis, all sequencing reads were mapped to NCBI build 37 (mm9) of the mouse genome using Bowtie2.
All mapped reads with high quality were filtered by “samtools view -q 40”. The potential PCR duplicated reads were removed by “samtools rmdup”.
The mapped sequencing reads were normalized as Counts Per Million Reads (CPM) using bamCoverage  --normalizeUsing CPM --extendReads 200.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: E14 mouse embryonic stem cells

growth_protocol: The  wild-type E14 mESCs with 3xFlag knock-in to the endogenous Kdm2b gene were maintained on the 0.1% gelatin coated plates in "2i" medium that contained 50% Neurobasal medium (Life Technologies) and 50% DMEM/F12 medium (Life Technologies) supplemented with 1x N2-supplement (Life Technologies), 1x B27 supplement (Life Technologies), 7.5% bovine serum albumin (Life Technologies), 1x GlutaMAX (Life Technologies), 1x beta-mercaptoethanol (Life Technologies), 1mM PD0325901, 3mM CHIR99021, 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore), and 100U/ml penicillin/streptomycin (Life Technologies). The PD culture conditoin is the same as 2i culture condtion except for it containng only 1mM PD0325901. The serum-containing mESC culture condition included DMEM medium (Life Technologies) supplemented with 100U/ml penicillin/streptomycin (Life Technologies), 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate (Life Technologies), 1x GlutaMAX (Life Technologies), 1x beta-mercaptoethanol (Life Technologies) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies.
ChIP DNA library was constructed for HiSeq4000 (Illumina) sequencing using NEBNext UltraII DNA library Prep Kit for Illumina (New England BioLabs, Inc) according to the manufacturer’s instructions. Adapter-ligated DNA was amplified by PCR for 12-14 cycles and followed by size selection using agarose gel electrophoresis. The DNA was purified using QIAquick gel extraction kit (Qiagen) and quantified both with an Agilent Bioanalyzer and Invitrogen Qubit. The DNA was diluted to a working concentration of 20nM prior to sequencing. Sequencing on an Illumina HiSeq4000 instrument was carried out by the Genomics Core Facility at Michigan State University.

tag: modification

value: 3xFlag knock-in to endogeous Kdm2b C-terminus

value: Erk1/Erk2 double knockout+Jarid2 transgene

tag: chip antibody


title: ChIP_Erkdko_ectopicJarid2_serum_H3K27m3

description: serum medium


title: ChIP_Erkdko_ectopicJarid2_serum_ezh2

description: serum medium

value: Ezh2 (Cell Signaling,5246, lot 1)


title: ChIP_Erkdko_ectopicJarid2_serum_jarid2

description: serum medium

value: Jarid2 (Cell Signaling, 13594, lot 1)


title: PNF_E18.5.C


title: ChIP_Erkdko_ectopicErk2_serum_H3K27m3

description: serum medium

value: Erk1/Erk2 double knockout+Erk2 transgene


title: A23_D.EPSCs_SmartSeq2

value: embryonic stem cells


title: A24_D.EPSCs_SmartSeq2


title: A22_D.EPSCs_SmartSeq2


title: ChIP_Erkdko_ectopicErk2_serum_jarid2

description: serum medium


title: ChIP_Erkdko_ectopicErk2_serum_input

description: serum medium


title: ChIP_Erkdko_ectopicErk2_serum_ezh2

description: serum medium


title: A21_D.EPSCs_SmartSeq2


title: A9_2i_SmartSeq2


title: A20_D.EPSCs_SmartSeq2


title: A2_2i_SmartSeq2


title: ChIP_Erkdko_serum_H3K27m3_rep2

description: serum medium

value: Erk1/Erk2 double knockout


title: A19_D.EPSCs_SmartSeq2


title: ChIP_Erkdko_serum_jarid2_rep2

description: serum medium


title: A17_D.EPSCs_SmartSeq2


title: ChIP_Erkdko_serum_jarid2_rep1

description: serum medium


title: A15_D.EPSCs_SmartSeq2


title: ChIP_Erkdko_serum_ezh2_rep2

description: serum medium


title: ChIP_Erkdko_serum_input_rep2

description: serum medium


title: ChIP_Erkdko_serum_ezh2_rep1

description: serum medium


title: A16_D.EPSCs_SmartSeq2


title: A14_D.EPSCs_SmartSeq2


title: ChIP_mESC_PD_catenin_rep1

description: serum-free medium with PD0325901

value: wild-type

value: beta-catenin (Cell Signaling, 8480, lot 5)


title: ChIP_Erkdko_serum_input_rep1

description: serum medium


title: A11_2i_SmartSeq2


title: ChIP_mESC_PD_catenin_rep2

description: serum-free medium with PD0325901


title: A13_D.EPSCs_SmartSeq2


title: A12_2i_SmartSeq2


title: A10_2i_SmartSeq2


title: ChIP_mESC_PD_Input_rep2

description: serum-free medium with PD0325901


title: ChIP_mESC_PD_Input_rep1

description: serum-free medium with PD0325901


title: A1_2i_SmartSeq2


title: SM99_E2.5_SmartSeq2

source_name: E2.5 embryo

value: E2.5 embryo

tag: developmental stage


title: ChIP_mESC_PD_H3K27me3_rep2

description: serum-free medium with PD0325901


title: ChIP_mESC_PD_jarid2_rep2

description: serum-free medium with PD0325901


title: SM97_E2.5_SmartSeq2


title: SM98_E2.5_SmartSeq2


title: ChIP_Erkdko_serum_H3K27m3_rep1

description: serum medium


title: ChIP_mESC_PD_jarid2_rep1

description: serum-free medium with PD0325901


title: A18_D.EPSCs_SmartSeq2


title: SM96_E2.5_SmartSeq2


title: ChIP_mESC_PD_H3K27me3_rep1

description: serum-free medium with PD0325901


title: ChIP_mESC_PD_ezh2_rep2

description: serum-free medium with PD0325901


title: ChIP_mESC_PD_ezh2_rep1

description: serum-free medium with PD0325901


title: SM93_E2.5_SmartSeq2


title: SM94_E2.5_SmartSeq2


title: SM92_E2.5_SmartSeq2


title: ChIP_mESC_serum_catenin_rep2

description: serum medium


title: SM91_E2.5_SmartSeq2


title: SM9_E4.5_SmartSeq2

source_name: E4.5 embryo

value: E4.5 embryo


title: SM89_E4.5_SmartSeq2


title: ChIP_mESC_serum_Kdm2b_rep1

description: serum medium

value: Flag (Sigma, F7425)


title: ChIP_mESC_serum_ring1b_rep2

description: serum medium

value: Ring1b (Cell Signling, 5694, lot1)


title: SM90_E2.5_SmartSeq2


title: ChIP_mESC_serum_jarid2_rep2

description: serum medium


title: ChIP_mESC_serum_jarid2_rep1

description: serum medium


title: ChIP_mESC_serum_Kdm2b_rep2

description: serum medium


title: ChIP_mESC_serum_ring1b_rep1

description: serum medium


title: SM88_E4.5_SmartSeq2


title: SM87_E4.5_SmartSeq2


title: SM86_E4.5_SmartSeq2


title: SM85_E4.5_SmartSeq2


title: SM83_E4.5_SmartSeq2


title: ChIP_mESC_serum_input_rep1

description: serum medium


title: ChIP_mESC_serum_H3k27me3_rep2

description: serum medium


title: SM95_E2.5_SmartSeq2


title: ChIP_mESC_serum_H3K27me3_rep1

description: serum medium


title: ChIP_mESC_serum_input_rep2

description: serum medium


title: SM82_E4.5_SmartSeq2


title: ChIP_mESC_serum_H3k4me3_rep2

description: serum medium

value: H3K4me3(Diagenode, C15410003, lot A1052D)


title: SM80_E4.5_SmartSeq2


title: SM8_E4.5_SmartSeq2


title: ChIP_mESC_serum_H3K4me3_rep1

description: serum medium


title: SM79_E4.5_SmartSeq2


title: SM78_E4.5_SmartSeq2


title: ChIP_mESC_serum_ezh2_rep2

description: serum medium

value: Ezh2 (Cell Signaling,5246, lot 1) H3K4me3(Diagenode, C15410003, lot A105Ezh2 (Cell Signaling,5246, lot 1) 2D)


title: ChIP_mESC_ectopicJarid2_2i_jarid2_rep2

description: 2i medium

value: Jarid2 transgene


title: ChIP_mESC_serum_ezh2_rep1

description: serum medium


title: ChIP_mESC_ectopicJarid2_2i_jarid2_rep1

description: 2i medium


title: ChIP_mESC_ectopicJarid2_2i_input_rep2

description: 2i medium


title: SM74_E4.5_SmartSeq2


title: SM77_E4.5_SmartSeq2


title: SM70_E4.5_SmartSeq2


title: ChIP_mESC_ectopicJarid2_2i_H3K27m3_rep2

description: 2i medium


title: SM76_E4.5_SmartSeq2


title: SM7_E4.5_SmartSeq2


title: ChIP_mESC_ectopicJarid2_2i_input_rep1

description: 2i medium


title: ChIP_mESC_ectopicJarid2_2i_ezh2_rep2

description: 2i medium


title: ChIP_mESC_ectopicJarid2_2i_H3K27m3_rep1

description: 2i medium


title: ChIP_mESC_ectopicJarid2_2i_ezh2_rep1

description: 2i medium


title: ChIP_mESC_2i_catenin_rep2

description: 2i medium


title: SM64_E4.5_SmartSeq2


title: ChIP_mESC_2i_ring1b_rep2

description: 2i medium

value: Ring1b (Cell Signaling, 5694, lot 1)


title: SM62_E4.5_SmartSeq2


title: SM61_E4.5_SmartSeq2


title: ChIP_mESC_2i_catenin_rep1

description: 2i medium

value: 3xFlag knock-in to endogeous Kdm2b C-terminus


title: ChIP_mESC_2i_ring1b_rep1

description: 2i medium


title: SM63_E4.5_SmartSeq2


title: SM60_E4.5_SmartSeq2


title: ChIP_mESC_2i_Kdm2b_rep2

description: 2i medium


title: ChIP_mESC_2i_Kdm2b_rep1

description: 2i medium


title: SM59_E4.5_SmartSeq2


title: ChIP_mESC_2i_jarid2_rep2

description: 2i medium


title: SM58_E4.5_SmartSeq2


title: SM57_E4.5_SmartSeq2


title: SM68_E4.5_SmartSeq2


title: ChIP_mESC_2i_jarid2_rep1

description: 2i medium


title: SM55_E4.5_SmartSeq2


title: SM56_E4.5_SmartSeq2


title: SM54_E4.5_SmartSeq2


title: ChIP_mESC_2i_H3K27me3_rep2

description: 2i medium


title: ChIP_mESC_2i_input_rep2

description: 2i medium


title: ChIP_mESC_2i_input_rep1

description: 2i medium


title: ChIP_mESC_2i_H3k27me3_rep1

description: 2i medium


title: SM66_E4.5_SmartSeq2


title: SM53_E4.5_SmartSeq2


title: ChIP_mESC_2i_H3k4me3_rep2

description: 2i medium


title: SM52_E4.5_SmartSeq2


title: ChIP_mESC_2i_H3k4me3__rep1

description: 2i medium


title: SM51_E4.5_SmartSeq2


title: SM50_E4.5_SmartSeq2


title: SM5_E4.5_SmartSeq2


title: SM45_E4.5_SmartSeq2


title: ChIP_mESC_2i_Ezh2_rep1

description: 2i medium


title: 25_RNAseq_Erkdko_ectopicERK2_serum_rep2

description:
serum medium
4_cuffdiffout_Erkdko_ectopicErk2_serum.diff

data_processing:
For the RNA-Seq data analysis, all sequencing reads were mapped to NCBI build 37 (mm9) of the mouse genome using Tophat2.
The mapped reads were normalized to reads as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
The differential gene expression was calculated by Cuffdiff program and the statistic cutoff for identification of differential gene expression is q < 0.05 and 1.5-fold RPKM change between samples.
Genome_build: mm9

extract_protocol:
RNA was extracted and purified from cells using QI shredder (Qiagen) and RNeasy (Qiagen) spin columns.
Total RNA (1 µg) was used to generate RNA-seq library using NEBNext Ultra Directional RNA library Prep Kit for Illumina (New England BioLabs, Inc) according to the manufacturer’s instructions. Adapter-ligated cDNA was amplified by PCR and followed by size selection using agarose gel electrophoresis. The DNA was purified using Qiaquick gel extraction kit (Qiagen) and quantified both with an Agilent Bioanalyzer and Invitrogen Qubit. The libraries were diluted to a working concentration of 10nM prior to sequencing. Sequencing on an Illumina HiSeq4000 instrument was carried out by the Genomics Core Facility at Michigan State University.

value: Erk1/Erk2-dKO+Erk2 rescue


title: 24_RNAseq_Erkdko_ectopicERK2_serum_rep1


title: SM47_E4.5_SmartSeq2


title: 23_RNAseq_Erkdko_serum_rep2


title: 22_RNAseq_Erkdko_serum_rep1


title: 21_RNAseq_mESC_ERKreactivation_12hr_rep3

description:
reactivation ERK 12hr
3_cuffdiffout_mESC_ERKreactivation_0_6_12.diff


title: SM43_E4.5_SmartSeq2


title: SM41_E4.5_SmartSeq2


title: 20_RNAseq_mESC_ERKreactivation_12hr_rep2


title: 18_RNAseq_mESC_ERKreactivation_6hr_rep3

description:
reactivation ERK 6hr
3_cuffdiffout_mESC_ERKreactivation_0_6_12.diff


title: SM40_E4.5_SmartSeq2


title: SM39_E4.5_SmartSeq2


title: SM38_E4.5_SmartSeq2


title: 17_RNAseq_mESC_ERKreactivation_6hr_rep2


title: 16_RNAseq_mESC_ERKreactivation_6hr_rep1


title: SM4_E4.5_SmartSeq2


title: 15_RNAseq_mESC_ERKreactivation_0hr_rep3

description:
reactivation ERK 0hr
3_cuffdiffout_mESC_ERKreactivation_0_6_12.diff


title: SM37_E4.5_SmartSeq2


title: ChIP_mESC_2i_Ezh2_rep2

description: 2i medium

value: Ezh2 (Cell Signaling,5246, lot 1)


title: 13_RNAseq_mESC_ERKreactivation_0hr_rep1


title: SM36_E4.5_SmartSeq2


title: 14_RNAseq_mESC_ERKreactivation_0hr_rep2


title: 12_RNAseq_mESC_ectopicJarid2_2i_rep3

description:
2i medium
2_cuffdiffout_mESC_serum_2i_ectopicJarid2.diff

value: ectoptic Jarid2 expression


title: SM44_E4.5_SmartSeq2


title: SM35_E4.5_SmartSeq2


title: SM33_E4.5_SmartSeq2


title: 11_RNAseq_mESC_ectopicJarid2_2i_rep2


title: SM31_E4.5_SmartSeq2


title: 9_RNAseq_mESC_PD_rep3

description:
serum-free medium with PD0325901
1_cuffdiffout_mESC_serum_2i_PD_gene_exp.diff


title: SM42_E4.5_SmartSeq2


title: 10_RNAseq_mESC_ectopicJarid2_2i_rep1


title: SM30_E4.5_SmartSeq2


title: SM34_E4.5_SmartSeq2


title: SM3_E4.5_SmartSeq2


title: 8_RNAseq_mESC_PD_rep2


title: 7_RNAseq_mESC_PD_rep1


title: 19_RNAseq_mESC_ERKreactivation_12hr_rep1


title: 5_RNAseq_mESC_serum_rep2

description:
serum medium
1_cuffdiffout_mESC_serum_2i_PD_gene_exp.diff


title: SM28_E4.5_SmartSeq2


title: 4_RNAseq_mESC_serum_rep1


title: SM29_E4.5_SmartSeq2


title: 3_RNAseq_mESC_2i_rep3

description:
2i medium
1_cuffdiffout_mESC_serum_2i_PD_gene_exp.diff


title: SM27_E4.5_SmartSeq2


title: SM26_E4.5_SmartSeq2


title: 2_RNAseq_mESC_2i_rep2


title: SM25_E4.5_SmartSeq2


title: SM24_E4.5_SmartSeq2


title: SM23_E4.5_SmartSeq2


title: SM21_E4.5_SmartSeq2


title: SM22_E4.5_SmartSeq2


title: GYV-6

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
Sample_95763
G=GnRH Immunoprecipitate, Y=young, V=vehicle, biological replicate = 6

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to verify sample quality.
The Tuxedo Suite was used to align reads to the reference transcriptome using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure only high quality data
Two different methods were used for expression quantitation, normalization, and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was one method used for expression quantitation and differential expression analysis. This analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
HTSeq (version 0.6.1)   to count non-ambiguously mapped reads only. Data were pre-filtered to remove genes with 0 counts in all samples. DESeq2 (version 1.14.1) for normalization and differential expression
Genome_build: mm10
Supplementary_files_format_and_content: text file of raw counts

molecule: polyA RNA

source_name: Preoptic area of the hypothalamus

growth_protocol: GnRH CRE (homozygote) male mice were bred to floxed-stop-floxed  L10a-GFP (homozygote) female mice to generate offspring that express GFP tagged ribosomal protein L10a in GnRH neurons.

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen; 74004) with on column DNasing and assessed for quantity and quality using the Pico or Nano Chip (Agilent).
SMARTer v4 Ultra low (poly A), fragment length 120nt.

treatment_protocol: Preoptic Area hypothalamic punches were collected from female  adult female (diestrous)  tissue collection from both sexes.

value: GnRH CRE x Floxed L10a-GFP

value: Preoptic area of the hypothalamus

tag: rna fraction

value: GnRH Enriched Immunoprecipitant

tag: age

value: Young

tag: prenatal treatment

value: Vehicle


title: GYD-6

description:
Sample_95762
G=GnRH Immunoprecipitate, Y=young, D=DHT, biological replicate = 6

value: DHT


title: GYV-5

description:
Sample_95760
G=GnRH Immunoprecipitate, Y=young, V=vehicle, biological replicate = 5


title: SM20_E4.5_SmartSeq2

tag: cell type

value: E4.5 embryo


title: SM2_E4.5_SmartSeq2


title: SM18_E4.5_SmartSeq2


title: 6_RNAseq_mESC_serum_rep3

value: wild-type


title: SM17_E4.5_SmartSeq2


title: TYD-5

description:
Sample_95756
T=total, Y=young, D=DHT, biological replicate = 5

value: GnRH Depleted Supernatant


title: SM32_E4.5_SmartSeq2


title: 1_RNAseq_mESC_2i_rep1


title: SM13_E4.5_SmartSeq2


title: GAD-6

description:
Sample_95753
G=GnRH Immunoprecipitate, A=adult, D=DHT, biological replicate = 6

value: Adult


title: SM15_E4.5_SmartSeq2


title: TYD-4

description:
Sample_95754
T=total, Y=young, D=DHT, biological replicate = 4


title: GAD-5

description:
Sample_95752
G=GnRH Immunoprecipitate, A=adult, D=DHT, biological replicate = 5


title: TYV-6

description:
Sample_95758
T=total, Y=young, V=vehicle, biological replicate = 6


title: GAV-5

description:
Sample_95751
G=GnRH Immunoprecipitate, V=vehicle, D=DHT, biological replicate = 5


title: GYD-4

description:
Sample_95759
G=GnRH Immunoprecipitate, Y=young, D=DHT, biological replicate = 4


title: GYD-5

description:
Sample_95761
G=GnRH Immunoprecipitate, Y=young, D=DHT, biological replicate = 5


title: GAV-4

description:
Sample_95750
G=GnRH Immunoprecipitate, V=vehicle, D=DHT, biological replicate = 4


title: GAV-3

description:
Sample_95749
G=GnRH Immunoprecipitate, V=vehicle, D=DHT, biological replicate = 3


title: SM118_E4.5_SmartSeq2


title: SM19_E4.5_SmartSeq2


title: SM119_E4.5_SmartSeq2


title: GAV-2

description:
Sample_95748
G=GnRH Immunoprecipitate, V=vehicle, D=DHT, biological replicate = 2


title: GAD-4

description:
Sample_95747
G=GnRH Immunoprecipitate, A=adult, D=DHT, biological replicate = 4


title: TYD-6

description:
Sample_95757
T=total, Y=young, D=DHT, biological replicate = 6


title: SM117_E4.5_SmartSeq2


title: SM16_E4.5_SmartSeq2


title: GAD-3

description:
Sample_95746
G=GnRH Immunoprecipitate, A=adult, D=DHT, biological replicate = 3


title: TYV-5

description:
Sample_95755
T=total, Y=young, V=vehicle, biological replicate = 5


title: GAD-2

description:
Sample_95745
G=GnRH Immunoprecipitate, A=adult, D=DHT, biological replicate = 2


title: SM14_E4.5_SmartSeq2


title: GAV-1

description:
Sample_95744
G=GnRH Immunoprecipitate, V=vehicle, D=DHT, biological replicate = 1


title: SM105_E2.5_SmartSeq2

value: E2.5 embryo


title: SM104_E2.5_SmartSeq2


title: GAD-1

description:
Sample_95743
G=GnRH Immunoprecipitate, A=adult, D=DHT, biological replicate = 1


title: SM12_E4.5_SmartSeq2


title: SM103_E2.5_SmartSeq2


title: ChIP_mESC_serum_catenin_rep1

description: serum medium

value: beta-catenin (Cell Signaling, 8480, lot 5)


title: SM101_E2.5_SmartSeq2


title: GYD-2

description:
Sample_95741
G=GnRH Immunoprecipitate, Y=young, D=DHT, biological replicate = 2


title: SM100_E2.5_SmartSeq2


title: SM11_E4.5_SmartSeq2


title: SM10_E4.5_SmartSeq2


title: SM107_E2.5_SmartSeq2


title: SM1_E4.5_SmartSeq2


title: GYV-4

description:
Sample_95740
G=GnRH Immunoprecipitate, Y=young, V=vehicle, biological replicate = 4


title: GYV-2

description:
Sample_95737
G=GnRH Immunoprecipitate, Y=young, V=vehicle, biological replicate = 2


title: GYD-1

description:
Sample_95739
G=GnRH Immunoprecipitate, Y=young, D=DHT, biological replicate = 1


title: GYV-3

description:
Sample_95738
G=GnRH Immunoprecipitate, Y=young, V=vehicle, biological replicate = 3


title: SM106_E2.5_SmartSeq2


title: GYV-1

description:
Sample_95736
G=GnRH Immunoprecicitate, Y=young, V=vehicle, biological replicate = 1


title: CC_SMC3_1

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

description:
cells sorted: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+
HET-CC-8

data_processing:
RNAseq fastq files were trimmed using Trim Galore and cutadapt to remove adapter sequences.
Trimmed fastq files were aligned using STAR (version 2.5.3a) to the mouse genome (mm10) using Gencode (version M12) transcriptome assembly.
Coding genes were quantified using subread featureCounts (v1.4.5-p1) to annotate uniquely mapped reads to Gencode annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts and tpm

source_name: centrocytes from spleen

growth_protocol: Mice were housed in HEPA-filtered ventilated racks in our animal facilities and received food and water ad libitum.

extract_protocol:
Cells were sorted into Trizol reagent (Invitrogen) and RNA was extracted following the manufacturer instructions. RNA quality was evaluated using Agilent Technologies 2100 Bioanalyzer and samples that passed the quality control (RNA Integrity Number ≥8) were subjected to library preparation
Library preparation, sequencing and post-processing of the raw data was performed at the Epigenomics Core at Weill Cornell Medicine. Illumina TruSeq RNA sample kits were used for libarary preparation, according to the manufacturer.

treatment_protocol: Mice were immunized with sheep red blood cells (SRBC) 8 days before extraction of spleens

value: centrocytes from spleen

tag: cell markers

value: 10 weeks

tag: littermate

value: litter 1


title: CC_WT_3

description:
cells sorted: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+
WT-CC-5


title: TAD-6

description:
Sample_95734
T=total, A=adult, D=DHT, biological replicate = 6


title: GYN

description:
Sample_95735
negative control

value: Floxed L10a-GFP

value: NoGFP


title: CC_WT_2

description:
cells sorted: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+
WT-CC-4


title: TAD-5

description:
Sample_95733
T=total, A=adult, D=DHT, biological replicate = 5

value: GnRH CRE x Floxed L10a-GFP


title: GYD-3

description:
Sample_95742
G=GnRH Immunoprecipitate, Y=young, D=DHT, biological replicate = 3

value: Preoptic area of the hypothalamus


title: MPC_11_OUAr_3: MPC_11_OUAr cells

data_processing:
Library strategy: HiC
Hi-C bench and HiCExplorer was used to process the fastq files into sparse contact matrices for analysis with R.
Filtered read pairs were also converted into mcool format using Cooler
Supplementary_files_format_and_content: Cooler format of contact matrices

source_name: ATCC

growth_protocol: THB-7 and MPC_11_OUAr cells were grown as recommended by the ATCC.

extract_protocol:
Cells were sorted into PBS and one million cells were subjected to in situ Hi-C protocol
In situ HiC protocol was performed

value: MPC_11_OUAr cells

value: wildtype

tag: cell population


title: TAV-4

description:
Sample_95731
T=total, V=vehicle, D=DHT, biological replicate = 4

value: Vehicle


title: THB-7_3: THB-7 cells

value: THB-7 cells


title: MPC_11_OUAr_1: MPC_11_OUAr cells


title: CC_SMC3_3

description:
cells sorted: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+
HET-CC-13


title: THB-7_2: THB-7 cells


title: CC_WT_1

description:
cells sorted: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+
WT-CC-3


title: TAD-4

description:
Sample_95728
T=total, A=adult, D=DHT, biological replicate = 4

value: DHT


title: TAV-5

description:
Sample_95732
T=total, V=vehicle, D=DHT, biological replicate = 5


title: TAD-3

description:
Sample_95727
T=total, A=adult, D=DHT, biological replicate = 3


title: TAV-3

description:
Sample_95730
T=total, V=vehicle, D=DHT, biological replicate = 3


title: THB-7_1: THB-7 cells


title: TAV-1

description:
Sample_95725
T=total, V=vehicle, D=DHT, biological replicate = 1


title: NBC_WT_2: DAPI-, B220+, Fas-, CD38+, IgD+

source_name: naïve b cells from spleen

value: naïve b cells from spleen


title: TAD-1

description:
Sample_95724
T=total, A=adult, D=DHT, biological replicate = 1

value: GnRH Depleted Supernatant


title: TYD-3

description:
Sample_95723
T=total, Y=young, D=DHT, biological replicate = 3

value: Young


title: NBC_WT_1: DAPI-, B220+, Fas-, CD38+, IgD+


title: TAD-2

description:
Sample_95726
T=total, A=adult, D=DHT, biological replicate = 2

value: Adult


title: TYD-2

description:
Sample_95722
T=total, Y=young, D=DHT, biological replicate = 2


title: CC_SMC3_1: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+


title: TYD-1

description:
Sample_95720
T=total, Y=young, D=DHT, biological replicate = 1


title: CC_WT_1: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+


title: TYV-3

description:
Sample_95719
T=total, Y=young, V=vehicle, biological replicate = 3


title: CB_SMC3_2: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+

value: DAPI-, B220+, Fas+, CD38-, CXCR4+ and CD86-


title: CC_SMC3_2: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+

value: centrocytes from spleen


title: TYV-4

description:
Sample_95721
T=total, Y=young, V=vehicle, biological replicate = 4


title: CB_SMC3_1: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+

value: 10 weeks


title: CC_WT_2: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+

value: litter 1


title: CB_WT_2: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+


title: TYV-2

description:
Sample_95718
T=total, Y=young, V=vehicle, biological replicate = 2


title: CB_WT_1: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+


title: CC_SMC3_2

description:
cells sorted: DAPI-, B220+, Fas+, CD38-, CXCR4- and CD86+
HET-CC-11


title: mouse scRNA-seq 2

value: Prrx-Cre

value: Postnatal ventral skin

value: Fibroblasts


title: mouse scRNA-seq 1


title: 1-SFO-single_cell_RNASeq

city: Dallas

first: Allan-Hermann

last: Pool

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

institute: University of Texas Southwestern Medical Center

data_processing:
Gene-cell matrices were generated by mapping sequencing reads to mm10 based mouse pre-mRNA reference transcriptome with Cell Ranger 3.0.1
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are simple gene-cell matrices (genes as rows, cell indexes as columns).

source_name: Dissociated single cell suspensions from SFO

extract_protocol:
Animals were anaesthetized with isoflurane. Brains were extracted and dissected in NMDG-ACSF. Tissue was digested with papain in trehalose-HEPES-ACSFand triturated to generate single cell suspensions. For stimulus to cell-type mapping experiments, actinomycin-D was included in NMDG-ACSF and trehalose-HEPES-ACSF to block artificial induction of immediate early genes.
Sequencing libraries were constructed following 10x Genomics 3' v2 (Samples 1, 2) or v3 )Samples 3-10) standard protocols.
3' Single-cell RNA-Seq

treatment_protocol: Samples 3, 7: water sated; Samples 4, 8: osmotic thirst (intraperitoneal (i.p.) injection of 2 M NaCl (5 μl/g bodyweight) followed by sacking 1 hour after injection); Samples 5, 9: hypovolemic thirst (i.p. injection of furosemide at a dose of 50 mg/kg bodyweight followed by sacking 4 hours after injection); Samples 6, 10: chronic water deprivation (36H water deprivation).

value: Subfornical organ (SFO)


title: 2-OVLT-single_cell_RNASeq

source_name: Dissociated single cell suspensions from OVLT

value: Vascular organ of the lamina terminalis (OVLT)


title: Enhancer cluster-KO RNA-seq Rep3

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

country: China

institute: Nankai University

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes counts values

source_name: RA induced Enhancer cluster-KO E14 differentiation 4 days  replicate 3

growth_protocol: Mouse ESCs E14 was cultured as the previous scheme with a few modifications. ESCs were grown in culture dishes coated with 0.1% gelatin (Sigma, Lot # SLBQ9498V) in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, Lot # 8119213) supplemented with 15% fetal bovine serum (FBS, AusGeneX, Lot # FBS00717-1), 100 nM nonessential amino acids (100x, Gibco, Lot # 2027433), 200 mM L-Glutamate (100x, Gibco, Lot # 2085472), 1% Penicillin-streptomycin (Gibco, Lot # 2029632), 50 μM β-mercaptoethanol (Sigma, Cas # 60-24-2), 10 ng/mL LIF (ESGRO, Lot # ESG1107), 1 μM PD0325901 (a MEK inhibitor, MedChemExpress, Lot # HY-10254) and 3 μM CHIR99021 (a GSK inhibitor, MedChemExpress, Lot # HY-10182). The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce ESCs differentiation, cells were gently washed with 1x phosphate buffer saline solution (PBS), dissociated and replanted at an appropriate density on gelatin-coated plates in LIF/2i withdrawal medium supplemented with 5 µm RA (Solarbio®, Lot # 1108F031) for 4 days. The culture medium was replaced at the given point-in-time.

value: Embryonic stem cells

tag: cell line

value: embryo, blastocyst embryo, blastocyst

tag: treatment

value: RA induced differentiation 4 days


title: Enhancer cluster-KO RNA-seq Rep2

source_name: RA induced Enhancer cluster-KO E14 differentiation 4 days  replicate 2

tag: tissue


title: H3 ChIP centroblast Cγ1-cre 3

description: cells sorted: DAPI-, B220+, FAS+, CD38-, CXCR4-, CD86+

data_processing:
The split reads were aligned using bwa mem to mm10. Duplicate marking and removal was done by Picard.
Peaking calling were preformed using two methods. The H3K27Ac peaks were called against H3 total as input uisng Homer package with following command:  findPeaks <K27Tag> -style histone 1000 -C 0 -o auto -i <H3_Tag>.
A consensus peaks were called using Genrich packages. All H3K27ac aligned files is provided as sample and H3 aligned files were provided as input to creat a concensus peak file.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized and scaled bigwigs and narrowpeak file

source_name: germinal center centrocytes from spleen

extract_protocol:
Mint-ChIP was performed using H3K27Ac antibody (Cat#39133, lot 31814008) from Active Motif following the protocol from the Berstein lab. Briefly, 50,000 FACS sorted centrocytes, in triplicates, were processed with MNase to fragment native chromatin.
Barcoded adapters were ligated to every sample and samples were multiplexed for chromatin immunoprecipitation (ChIP). After ChIP, material was linearly amplified by RNA in vitro transcription in the presence of RNAse inhibitor RNAseOUT (Invitrogen 10777019). Fragments were reverse-transcribed and amplified as a library

value: germinal center centrocytes from spleen

value: 3-4 months

value: mixed litters


title: MPC_11_OUAr_2: MPC_11_OUAr cells

value: MPC_11_OUAr cells

value: wildtype


title: WT RNA-seq Rep3

source_name: RA induced E14 differentiation 4 days  replicate 3


title: Enhancer cluster-KO RNA-seq Rep1

source_name: RA induced Enhancer cluster-KO E14 differentiation 4 days  replicate 1


title: WT RNA-seq Rep2

source_name: RA induced E14 differentiation 4 days  replicate 2


title: WT and SMC single cells

description: cells sorted: YFP+,IgD-

data_processing:
Seven Bridges Rhapsody Analysis Pipeline version 1.3
Seven Bridges Rhapsody pipeline trimmed adaptor sequences and identified UMI and cellular barcodes. R1 contains the cell barcode. Please see the file "barcode_location.txt" for an explanation of the barcode composition.
Seven Bridges Rhapsody pipeline aligned sequences to a reference file containing the sequences of targeted genes
Seven Bridges Rhapsody pipleine filtered reads based on RSEC UMI adjustment
Genome_build: Seven Bridges Rhapsody pipleine filtered reads based on DBEC UMI adjustment
Supplementary_files_format_and_content: Matrix of gene counts per cell in csv format

source_name: germinal center and post-germinal center B-cells from spleen with genotype R26wt/LSL-YFP;Cγ1wt/cre and R26wt/LSL-YFP;Smc3fl/wt;Cγ1wt/cre

extract_protocol:
Cells were sorted into PBS and ten thousand cells from each spleen were subjected to single cell RNA-seq using BDRhapsody platform
Library preparation for single cell, sequencing and post-processing of the raw data was performed at Weill Cornell Medicine. Libraries were prepared according to BD Rhapsody specifications.

value: B-cells from spleen

value: mixed sample (non-demultiplexed) includes WT and SMC


title: UUO_D5, KO (BW_33)

first: George

middle: Edward

last: Marti

address: 318 Campus Dr., E300

department: MCP

data_processing:
Sequences were aligned to GRCm38 (from ensembl) on the Stanford Sherlock cluster with STAR and saved to a BAM file using the commands STAR --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM Unsorted  --quantMode GeneCounts
BAM files were sorted with samtools and transcripts were counted with the command "python3 -m HTSeq.scripts.count -f bam -s no -r name -t exon --additional-attr=gene_name"
Counts were merged into single tsv file using a custom made python script.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited gene counts for every sample

source_name: left kidney

extract_protocol:
Total RNA was isolated from fresh frozen kidney tissues using an Allprep DNA/RNA mini kit (Qiagen) and analyzed using an Agilent Bioanalyzer (Agilent Technloogies) for quality control.
Libraries were constructed with PrepX mRNA library kit (WaferGen) and sequenced to 50 bp using TruSeq SBS kit on Illumina Hiseq system.

treatment_protocol: Surgically induced UUO was generated by applying a nontraumatic microvascular clamp on the left ureter in 8–12-week-old Sprr2f-KO mice. Left kidneys were harvested 0 and 5 days after obstruction.  They were bisected, with half fixed in formalin overnight for subsequent sectioning, and half frozen quickly on crushed dry ice before being transferred to a -80°C freezer for RNA isolation.

value: Sprr2f KO

value: UUO

tag: time


title: H3K27Ac ChIP centroblast Cγ1-cre 3


title: H3 ChIP centroblast Cγ1-cre 2


title: WT RNA-seq Rep1

source_name: RA induced E14 differentiation 4 days  replicate 1


title: UUO_D0, WT (BW_34)

value: WT


title: UUO_D0, KO (BW_30)


title: H3K27Ac ChIP centroblast Cγ1-cre 2


title: H3 ChIP centroblast Cγ1-cre 1


title: RIP-seq of sample after 12h of LPS treatment rep 3

city: Seoul

first: Boyoun

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

department: Systems biology

country: South Korea

institute: Yonsei University

data_processing:
RNA-seq paired-end reads were mapped to UCSC mm10 Mus musculus genome using Tophat2
Exon-regions and intron-regions (GTF files) were identified using GenomicFeature R-package
The expression level of each gene was quantified as TPM using StringTie tool v2.1.3
RIP-seq paired-end reads were mapped to UCSC mm10 Mus musculus genome using Tophat2
The FPKM values of each gene (exon and intron, respectively) was quantified using StringTie tool v2.1.3
Genome_build: UCSC mm10 Mus musculus genome
Supplementary_files_format_and_content: tpm_all.200603.3.xlsx contains TPM values of each sample for exon and intron, respectively.

source_name: nucleus

extract_protocol:
Cytoplasm, nucleoplasm, and nucleoli were extracted from LPS-stimulated macrophages as previously described (http://www.lamondlab.com/f5nucleolarprotocol.htm).  RNAs were purifed using RiboEx reagent and cleaned up using RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Raw264.7 cells

tag: antibody

value: anti-Nucleolin antibody

value: LPS 12h


title: TYN

description:
Sample_95716
negative control

value: Floxed L10a-GFP

value: Preoptic area of the hypothalamus

value: GnRH Depleted Supernatant

value: Young

value: NoGFP


title: UUO_D0, KO (BW_29)

tag: strain


title: RIP-seq of sample after 2h of LPS treatment rep 3

value: LPS 2h


title: RIP-seq of sample after 12h of LPS treatment rep 2


title: UUO_D0, KO (BW_28)

tag: genotype


title: H3K27Ac ChIP centroblast Cγ1-cre 1

value: germinal center centrocytes from spleen

value: 3-4 months

value: mixed litters


title: UUO_D0, WT (BW_39)


title: miRNA_EC4

city: Shanghai

first: Zheyu

last: Zhang

address: Yueyang Road

institute: CAS

description:
These mice were not injected with LLC cells and thus do not have xenografted tumors.
processed data 3.txt

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads
the trimmed reads were aligned to merged pre-miRNA databases,using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression
The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.
Genome_build: miRBase v21
Supplementary_files_format_and_content: text files include TPM values for each Sample

source_name: germ-free mice were inoculated by gavage with Probiotics EcN

extract_protocol:
RNA was harvested using Trizol reagent.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps：1) 3'-adaptor ligation;2) 5'-adaptor ligation3) cDNA synthesis;4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).

value: plasma

tag: Sex

value: male


title: RIP-seq of sample after 2h of LPS treatment rep 2


title: RIP-seq of sample after 0h of LPS treatment rep 2

value: LPS 0h


title: UUO_D5, KO (BW_25)

value: Sprr2f KO

value: UUO


title: RIP-seq of sample after 0h of LPS treatment rep 3

value: Raw264.7 cells


title: miRNA_EC3


title: UUO_D0, KO (BW_31)


title: RIP-seq of sample after 0h of LPS treatment rep 1

value: anti-Nucleolin antibody


title: RNA-seq of cytosol after 15h of LPS treatment rep 3

source_name: cytoplasm

value: LPS 15h


title: UUO_D5, WT (BW_24)

value: WT


title: UUO_D5, WT (BW_21)


title: miRNA_EC2


title: miRNA_SPF-ABT-4

description:
These mice were not injected with LLC cells and thus do not have xenografted tumors.
processed data 2.txt

source_name: specific pathogen free (SPF) mice with broad-spectrum antibiotics (ABX) treatment


title: RNA-seq of cytosol after 15h of LPS treatment rep 2


title: RNA-seq of cytosol after 15h of LPS treatment rep 1


title: RIP-seq of sample after 12h of LPS treatment rep 1

value: LPS 12h


title: UUO_D5, KO (BW_20)


title: RNA-seq of cytosol after 12h of LPS treatment rep 2


title: RNA-seq of cytosol after 12h of LPS treatment rep 3


title: RNA-seq of cytosol after 12h of LPS treatment rep 1


title: UUO_D5, WT (BW_19)


title: RNA-seq of cytosol after 6h of LPS treatment rep 3

value: LPS 6h


title: miRNA_SPF-ABT-3


title: miRNA_SPF-ABT-1


title: RNA-seq of cytosol after 6h of LPS treatment rep 2


title: RIP-seq of sample after 2h of LPS treatment rep 1


title: ESC_D15_2

description: GC059147_ESC_D15_M_CGATGT.180531.HiSeq4000.FCA.lane8.gcap_17_11

tag: cell type source

value: ESCs

tag: timepoint


title: RNA-seq of cytosol after 6h of LPS treatment rep 1


title: miRNA_GF-Bifido3

source_name: germ-free mice were inoculated by gavage with Probiotics Bifidobacterium


title: ESC_D15_1

description: GC059147_ESC_D15_M_CGATGT.180531.HiSeq4000.FCA.lane7.gcap_17_11


title: miRNA_GF-Bifido2


title: RNA-seq of cytosol after 2h of LPS treatment rep 1


title: L_EPSC_D15_1

description: GC059147_EPSC_D15_M_GTGAAA.180531.HiSeq4000.FCA.lane7.gcap_17_11


title: miRNA_GF-Bifido1


title: L_EPSC_D15_2

description: GC059147_EPSC_D15_M_GTGAAA.180531.HiSeq4000.FCA.lane8.gcap_17_11


title: L_EPSC_D13_2

description: GC059147_EPSC_D13_M_CCGTCC.180531.HiSeq4000.FCA.lane8.gcap_17_11


title: RNA-seq of cytosol after 0h of LPS treatment rep 1


title: RNA-seq of cytosol after 0h of LPS treatment rep 2


title: miRNA_GF2

source_name: germ-free mice


title: L_EPSC_D13_1

description: GC059147_EPSC_D13_M_CCGTCC.180531.HiSeq4000.FCA.lane7.gcap_17_11


title: miRNA_GF1


title: RNA-seq of nucleoli after 15h of LPS treatment rep 3

source_name: nucleoli


title: RNA-seq of cytosol after 0h of LPS treatment rep 3


title: L_EPSC_D11_2

description: GC059147_EPSC_D11_M_AGTTCC.180531.HiSeq4000.FCA.lane8.gcap_17_11


title: sRNA_seq_AGO_IP_PrimaryPolyp_IgG_I

city: Maale-AdumimJerusalem

first: Arie

last: Fridrich

state: Israel

department: EEB

country: Israel

institute: The Hebrew University of Jerusalem

description:
small RNA
sRNA-seq-protocol-modified-nebnext

data_processing:
The data were pre-processed to remove the adapters using cutadapt
processed reads were analysed using miRDeep2 software
The gene models can be found here: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Genome_build: ASM20922v1, INSDC Assembly GCA_000209225.1, Sep 2007.
Supplementary_files_format_and_content: read counts
Supplementary_files_format_and_content: counts.tabular_tabular

organism: Nematostella vectensis

source_name: RNA extracted from immunoprecipitated AGO

extract_protocol: sRNA-seq-Zamore-protocol:Small RNA libraries were constructed as described in Phillip Zamore Lab Illumina TruSeq Small RNA Cloning Protocol April, 2014 (http://www.umassmed.edu/zamore/resources/protocols/).  sRNA-seq-modified-nebnext was carried out using NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (cat. no E7300, New Enagland Biolabs) according to the protocol described by: Plotnikova et al. Plant Cell 2019. mRNA sequensing was carried out with Lexogen Sense kit according to the manufacturer's instructions.

tag: developmental stage

value: Primary polyp

value: AGO


title: sRNA_seq_AGO_IP_PrimaryPolyp_AGO2_II


title: L_EPSC_D11_1

description: GC059147_EPSC_D11_M_AGTTCC.180531.HiSeq4000.FCA.lane7.gcap_17_11

data_processing:
Sequencing reads were mapped to mm10 reference genome using STAR 2.5.3a (Dobin et al., 2013). On average, 77,16% of reads were uniquely mapped and only those were kept for further analyses. Subsequently, the featureCounts function from the R Bioconductor package “Rsubread” (version 1.5.2) (Liao et al. 2019) was used to assign mapped reads to genomic features.
DESeq2 package and the associated protocol (Love et al. 2014) was used. Only genes that express at least 10 reads in total across all libraries were retained. PCA was performed using plotPCA function from the DESeq2 package with input of top 500 most variable genes after rlog transformation. Unless mentioned otherwise, gene expression was presented as log2 values after size-factor normalization for the differences in library size (DESeq2).
Smart-Seq2 read files (E2.5 and E4.5 embryos, and three pluripotent stem cell conditions: ESCs cultured in 2iLif, L-EPSCs, and D-EPSCs) were mapped to the mouse reference genome (mm10) using STAR aligner and only uniquely mapped reads were used for expression level estimation as reads per kilobase of gene model and million mappable reads (RPKMs) using RefSeq annotation.
Loom files were generated using export2loom function from pySCENIC package (0.9.15)
Genome_build: mm10
Supplementary_files_format_and_content: bulk_norm.csv
RPKM_matrix.txt
Loom files containing processed, normalized expression, regulon activity and clustering metadata, as well as UMAP embeddings.

extract_protocol:
Total RNA was isolated from 2iLif ESCs and L-EPSCs reprogramming intermediates at indicated days using TRIzol reagent according to manufacturer’s protocol.
4 µg of total RNA was used to generate libraries using of stranded poly(A) mRNA-Seq library with the KAPA stranded mRNA Library prep kit (KAPA Biosystems, KK8421). Libraries concentration was quantified with Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Q32854), and the final pool was generated by combining individual libraries in equimolar ratio. Libraries were sequenced on an Illumina HiSeq 4000 instrument (Illumina) with 51 bp reads and read depth ranging ~33 mln reads.
Single-cells from stem cells were sorted by FACS into 384 well plates containing lysis and RT, whereas embryo cells were manually picked and directly dispensed into lysis buffer containing RT. The current study generated cDNA libraries using the Smart-seq2 protocol.


title: sRNA_seq_AGO_IP_PrimaryPolyp_IgG_II


title: RNA-seq of nucleoli after 15h of LPS treatment rep 1


title: RNA-seq of nucleoli after 15h of LPS treatment rep 2


title: RNA-seq of cytosol after 2h of LPS treatment rep 2

value: LPS 2h


title: L_EPSC_D9_2

description: GC059147_EPSC_D9_M_CTTGTA.180531.HiSeq4000.FCA.lane8.gcap_17_11


title: RNA-seq of nucleoli after 12h of LPS treatment rep 3


title: RNA-seq of cytosol after 2h of LPS treatment rep 3


title: sRNA_seq_AGO_IP_PrimaryPolyp_AGO2_I


title: L_EPSC_D9_1

description: GC059147_EPSC_D9_M_CTTGTA.180531.HiSeq4000.FCA.lane7.gcap_17_11


title: miRNA_GF3


title: RNA-seq of nucleoli after 12h of LPS treatment rep 2


title: HeLa cells - IgG

city: Beijing

first: Ting

address: Taiping Road 27

institute: National Center of Biomedical Analysis

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.3.4 with default parameters
Data were filtered using the following specification: aligned bam files were first sorted with samtools and then duplicated reads  were removed with PICARD.
peaks were called using macs2 version 2.2.5 with the following setting: macs2 callpeak -g hs.
Genome_build: hg19
Supplementary_files_format_and_content: peak text file

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's standard protocol.

treatment_protocol: no-treatment

value: HeLa stable cell line

value: untreated

tag: chip antibody

value: IgG (Cell Signaling, 2729)


title: HeLa cells - Input


title: sRNA_seq_AGO_IP_PrimaryPolyp_AGO1_I


title: sRNA_seq_AGO_IP_PrimaryPolyp_AGO1_II


title: RNA-seq of nucleoli after 12h of LPS treatment rep 1


title: L_EPSC_D7_2

description: GC059147_EPSC_D7_M_TAGCTT.180531.HiSeq4000.FCA.lane8.gcap_17_11


title: HeLa cells - KANSL1

value: KANSL1 (Abnova, PAB20355; lot  A114005)


title: Kidney Tregs after cGN induction, rep2

city: Fukuoka

first: Minako

last: Ito

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

country: Japan

institute: Kyushu University

hyb_protocol: Expression Hybridization Kit (Agilent)

scan_protocol: DNA Microarray Scanner (2505C, Agilent), Gene Expression Wash Pack (Agilent)

data_processing:
Feature Extraction ver 10.7.1.1 (Agielnt)
GeneSpring GX 14.5 (Agilent), Threshold raw signals: 1.0, Normalization algorithm: Percentile Shift, Percentile target: 75

source_name: Tregs from renal tissue

label_protocol: One-Color RNA Spike-In Kit, Low Input Quick Amp Labeling Kit (Agilent)

extract_protocol: Tregs (CD45+CD3e+CD4+FoxP3-hCD2+ T cells) from renal tissue were isolated on day 28 after cGN induction. Total RNA was isolated using a TRIzol LS reagent (Invitrogen).

treatment_protocol: Tregs (CD45+CD3e+CD4+FoxP3-hCD2+ T cells) from renal tissue were isolated on day 28 after cGN induction. Disease severity was depended on variation among lots of anti-GBM antibodies in this experiments. To improve the quality of this analysis, we used the two lots of anti-GBM antibodies, M and I.

value: cGN induction

value: renal tissue

value: Treg

tag: anti-gbm antibody

value: M


title: sRNA_seq_AGO_IP_EarlyPlanula_IgG_II

value: Early planula


title: RNA-seq of nucleoli after 6h of LPS treatment rep 3

value: Raw264.7 cells


title: L_EPSC_D5_2

description: GC059147_EPSC_D5_M_ACTTGA.180531.HiSeq4000.FCA.lane8.gcap_17_11


title: sRNA_seq_AGO_IP_EarlyPlanula_IgG_I


title: RNA-seq of nucleoli after 6h of LPS treatment rep 2


title: sRNA_seq_AGO_IP_EarlyPlanula_AGO2_II


title: Tumor3_miRNA-seq

city: Hangzhou

first: Junfen

last: Xu

state: Other (Non U.S.)

address: No.1 Xueshi Road

department: Department of Gynecologic Oncology

institute: Women’s Hospital, Zhejiang University School of Medicine

description:
T_181 / CA3
T181_S13_L008
processed data file: All.Counts.miRNA.txt

data_processing:
RNA-seq: Reads filtering under criteria removing reads with 20% of the base quality lower than 13
RNA-seq: HISAT2.1.0 mapping to reference genome
RNA-seq: count counting
miRNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 33bp c) adaptor sequence.
miRNA-seq: Utilizing the BWA software, we mapped the clean data to mature miRNAs with annotation from miRBase(v.22).
miRNA-seq: count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: cervical adenocarcinoma tissue

extract_protocol:
RNA-seq: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.Part of RNA was utilized to construct rRNA depletion(NEBNext Ultra Directional RNA Library Prep Kit),The RNA with RIN >8.0 is right for cDNA library construction.
miRNA-seq: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols
miRNA-seq: miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject age

tag: tissue type

value: cervical adenocarcinoma tissue

tag: figo stage

tag: pathological grade

tag: tumor size

tag: lymph nodes metastasis

tag: molecule subtype

value: miRNA


title: L_EPSC_D5_1

description: GC059147_EPSC_D5_M_ACTTGA.180531.HiSeq4000.FCA.lane7.gcap_17_11


title: L_EPSC_D3_2

description: GC059147_EPSC_D3_M_GCCAAT.180531.HiSeq4000.FCA.lane8.gcap_17_11


title: RNA-seq of nucleoli after 6h of LPS treatment rep 1

tag: cell line

tag: treatment

value: LPS 6h


title: Tumor2_miRNA-seq

description:
T_111 / CA2
T111_S16_L008
processed data file: All.Counts.miRNA.txt


title: sRNA_seq_AGO_IP_EarlyPlanula_AGO2_I

tag: antibody


title: RNA-seq of nucleoli after 2h of LPS treatment rep 3


title: L_EPSC_D3_1

description: GC059147_EPSC_D3_M_GCCAAT.180531.HiSeq4000.FCA.lane7.gcap_17_11

value: ESCs


title: RNA-seq of nucleoli after 2h of LPS treatment rep 2


title: sRNA_seq_AGO_IP_EarlyPlanula_AGO1_I


title: Norm4_miRNA-seq

description:
N_3541 / N4
N3541_S8_L008
processed data file: All.Counts.miRNA.txt

source_name: normal cervical tissue

value: normal cervical tissue


title: Tumor1_miRNA-seq

description:
T_063 / CA1
T063_S15_L008
processed data file: All.Counts.miRNA.txt


title: sRNA_seq_AGO_IP_EarlyPlanula_AGO1_II

value: AGO


title: L_EPSC_D0_2

description: GC059147_EPSC_D0_M_TGACCA.180531.HiSeq4000.FCA.lane8.gcap_17_11


title: L_EPSC_D7_1

description: GC059147_EPSC_D7_M_TAGCTT.180531.HiSeq4000.FCA.lane7.gcap_17_11


title: Kidney Tregs after cGN induction, rep1

tag: tissue

tag: cell type

value: I


title: sRNA_seq_AGO_IP_AdultMale_IgG_II

value: Adult male


title: Tumor4_miRNA-seq

description:
T_202 / CA4
T202_S14_L008
processed data file: All.Counts.miRNA.txt


title: L_EPSC_D0_1

description: GC059147_EPSC_D0_M_TGACCA.180531.HiSeq4000.FCA.lane7.gcap_17_11

tag: cell type source


title: RNA-seq of nucleoli after 2h of LPS treatment rep 1

value: LPS 2h


title: Norm2_miRNA-seq

description:
N_1663 / N1
N1663_S9_L008
processed data file: All.Counts.miRNA.txt


title: Norm3_miRNA-seq

description:
N_2639 / N3
N2639_S11_L008
processed data file: All.Counts.miRNA.txt


title: RNA-seq of nucleoli after 0h of LPS treatment rep 3

value: LPS 0h


title: sRNA_seq_AGO_IP_AdultMale_IgG_I

description:
small RNA
sRNA-seq-protocol-modified-nebnext


title: mRNA_GF-Bifi4

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer
Total RNA of each sample was used to prepare the RNA sequencing library

treatment_protocol: Lung-metastasis model of mice: One million Lewis lung carcinoma (LLC) cells in 100 ul sterile PBS were injected into mice via tail vein.

value: tumor tissue

tag: tumor model

value: Lung-metastasis model of mice

tag: injected cell line

value: Lewis lung carcinoma (LLC)

tag: Sex

value: male


title: Norm1_miRNA-seq

description:
N_1134 / N1
N1134_S10_L008
processed data file: All.Counts.miRNA.txt


title: TAV-2

description:
Sample_95729
T=total, V=vehicle, D=DHT, biological replicate = 2

source_name: Preoptic area of the hypothalamus

tag: genotype

value: GnRH CRE x Floxed L10a-GFP

value: Preoptic area of the hypothalamus

tag: rna fraction

value: GnRH Depleted Supernatant

tag: age

value: Adult

tag: prenatal treatment

value: Vehicle


title: sRNA_seq_AGO_IP_AdultMale_AGO2_I

tag: developmental stage


title: RNA-seq of nucleoli after 0h of LPS treatment rep 2

value: Raw264.7 cells


title: mRNA_GF-Bifi3


title: mRNA_GF-Bifi2


title: RNA-seq of nucleus after 15h of LPS treatment rep 3

source_name: nucleoplasm

value: LPS 15h


title: RNA-seq of nucleoli after 0h of LPS treatment rep 1


title: Tumor4

description:
T_202 / CA4
T202_S45_L008
processed data file: All.counts.RNA.txt

tag: subject age

tag: tissue type

value: cervical adenocarcinoma tissue

tag: figo stage

tag: pathological grade

tag: tumor size


title: sRNA_seq_AGO_IP_AdultMale_AGO2_2

tag: antibody

value: AGO


title: Tumor3

description:
T_181 / CA3
T181_S44_L008
processed data file: All.counts.RNA.txt

tag: lymph nodes metastasis


title: mRNA_GF4

tag: tissue


title: RNA-seq of nucleus after 15h of LPS treatment rep 2

tag: cell line

tag: treatment


title: sRNA_seq_AGO_IP_AdultMale_AGO1_II


title: sRNA_seq_AGO_IP_AdultMale_AGO1_I


title: Tumor2

description:
T_111 / CA2
T111_S47_L008
processed data file: All.counts.RNA.txt


title: mRNA_GF2

tag: tumor model

tag: injected cell line


title: Tumor1

description:
T_063 / CA1
T063_S46_L008
processed data file: All.counts.RNA.txt


title: mRNA_GF1

tag: Sex


title: RNA-seq of nucleus after 15h of LPS treatment rep 1


title: KDsRNAseq_Control2_III

description:
small RNA
sRNA-seq-Zamore-protocol

source_name: whole animals

value: Planula

tag: agent

value: Morpholino


title: Norm4

description:
N_3541 / N4
N_3541_S39_L008
processed data file: All.counts.RNA.txt

value: normal cervical tissue


title: RNA-seq of nucleus after 12h of LPS treatment rep 3

value: LPS 12h


title: KDsRNAseq_Control2_II

description:
small RNA
sRNA-seq-Zamore-protocol


title: Norm3

description:
N_2639 / N3
N2639_S42_L008
processed data file: All.counts.RNA.txt


title: RNA-seq of nucleus after 12h of LPS treatment rep 2


title: mRNA_GF+SPF4

source_name: with fecal microbiota gavage transplantation (FMT) from specific pathogen free (SPF) mice into germ-free mice

value: tumor tissue


title: mRNA_GF+SPF2

value: Lung-metastasis model of mice


title: RNA-seq of nucleus after 12h of LPS treatment rep 1


title: Norm2

description:
N_1663 / N1
N_1663_S40_L008
processed data file: All.counts.RNA.txt


title: RNA-seq of nucleus after 6h of LPS treatment rep 3

value: LPS 6h


title: mRNA_GF+SPF1

value: Lewis lung carcinoma (LLC)

value: male


title: KDsRNAseq_Control1_III

description:
small RNA
sRNA-seq-Zamore-protocol


title: Norm1

description:
N_1134 / N1
N_1134_S41_L001
processed data file: All.counts.RNA.txt


title: KDsRNAseq_Control1_II

description:
small RNA
sRNA-seq-Zamore-protocol


title: RNA-seq of nucleus after 6h of LPS treatment rep 2


title: wt1

first: Yanqiu

last: Wang

address: 197 Rui-jin 2nd Road, Shanghai 20025, CHINA.

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

data_processing:
paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4)
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Genome_build: mm10
Supplementary_files_format_and_content: excel format

source_name: islet

extract_protocol:
Islet total RNA was extracted using a RNeasy Micro kit (Qiagen) following the manufacturer’s protocol.
RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

value: islet

tag: strain

tag: age

value: 2 week

tag: genotype/variation

value: wild type


title: KDsRNAseq_AGO2_III

description:
small RNA
sRNA-seq-Zamore-protocol

tag: developmental stage


title: KDsRNAseq_Control1_I

description:
small RNA
sRNA-seq-Zamore-protocol


title: RNA-seq of nucleus after 6h of LPS treatment rep 1


title: wt2


title: ko2

value: Ngn3Mettls KO


title: KDsRNAseq_AGO2_II

description:
small RNA
sRNA-seq-Zamore-protocol


title: RNA-seq of nucleus after 2h of LPS treatment rep 1

value: Raw264.7 cells

value: LPS 2h


title: RNA-seq of nucleus after 2h of LPS treatment rep 2


title: Islet-2w.IP

description: library strategy: MeRIP-Seq

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
clean reads of all libraries were aligned to the reference genome(MM10) by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software
Differentially methylated sites were identified by diffReps
Genome_build: mm10
Supplementary_files_format_and_content: excel format

extract_protocol:
Islet total RNA was extracted using a RNeasy Micro kit (Qiagen) following the manufacturer’s protocol.Briefly, 500 ug of fragmented mRNAs were incubated with 5 ug of anti- m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer (150 mM NaCl, 0.1% NP-40, 10 mM Tris–HCl, pH 7.4) for 2 h at 4◦C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4◦C for an additional 2 h. Then, bound mRNAs were eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction.
Purified mRNAs were used for RNA-seq library generation Purified mRNAs were used for RNA-seq library. Briefly, m6A RNA immunoprecipitation was performed with the GenSeq™ m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.with NEBNext® UltraTM RNA Library Prep Kit (NEB). Both the input sample (with- out immunoprecipitation) and the m6A IP sample were sub- jected to 150 bp paired-end sequencing on Illumina HiSeq sequencer. Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3′ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The reads were aligned to the reference genome (UCSC HG19) with Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified MACS software. Differentially methylated sites on RNAs were identified by diffReps. These peaks identified were mapped to transcriptome using home-made scripts.


title: KDsRNAseq_AGO2_I

description:
small RNA
sRNA-seq-Zamore-protocol


title: ko1


title: KDsRNAseq_Control2_I

description:
small RNA
sRNA-seq-Zamore-protocol


title: Islet-2w.Input

description: library strategy: MeRIP-Seq


title: RNA-seq of nucleus after 2h of LPS treatment rep 3


title: KDsRNAseq_AGO1_II

description:
small RNA
sRNA-seq-Zamore-protocol


title: RNA-seq of nucleus after 0h of LPS treatment rep 3

value: LPS 0h


title: KDsRNAseq_AGO1_I

description:
small RNA
sRNA-seq-Zamore-protocol