title: U33GW Right Medulla Oblongata

description:
Library name: U7
U33GW Right Medulla Oblongata


title: U33GW Left Medulla Oblongata

status: Public on Dec 17 2025

type: SRA

city: Jinan

first: ChengXin

last: Liu

state: Shandong

address: No. 16766, Jingshi Road

department: Cheeloo College of Medicine

country: China

institute: Shandong University

description:
Library name: U6
U33GW Left Medulla Oblongata

library_source: transcriptomic

data_processing:
SOAPnuke was used to remove adapter-containing reads, low-quality reads, and reads with high N content.
Clean reads were aligned to the reference genome using HISAT2.
Ericscript and rMATS were used for fusion genes and differential splicing analysis.
Bowtie2 was used to align reads to the gene set.
RSEM was used for gene expression quantification.
Assembly: GRCh38.p13
Supplementary files format and content: csv file include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: brainstem

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen) according to the manual instruction.Tissue was ground under liquid nitrogen, mixed with TRIzol, centrifuged, and treated with chloroform/isoamyl alcohol. RNA was precipitated with isopropanol, washed with ethanol, and dissolved in DEPC-treated water. RNA quality was assessed using Fragment Analyzer, Agilent 2100 Bioanalyzer, or Qseq-400.
Library preparation was performed using the Optimal Dual-mode mRNA Library Prep Kit (BGI) following manufacturer's protocols.

tag: tissue

value: brainstem


description:
Library name: V1
V24GW Central Lower Part Of The Medulla Oblongata


title: V24GW Left Upper Midbrain

description:
Library name: V6
V24GW Left Upper Midbrain


title: U33GW Left Lower Pons

description:
Library name: U5
U33GW Left Lower Pons


description:
Library name: V2
V24GW Middle Part Of The Left Medulla Oblongata


title: U33GW Right Midbrain

description:
Library name: U1
U33GW Right Midbrain


title: T12GW Medulla Oblongata

description:
Library name: T4
T12GW Medulla Oblongata


title: T12GW Pons

description:
Library name: T3
T12GW Pons


title: Damaged Muscle EV Rep 1

status: Public on Dec 18 2025

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

library_source: other

data_processing:
Quality control was performed using fastqc
Reads were aligned to the UCSC mm10 genome using version bwa
miRNA expression was quantified using featureCounts
Assembly: mm10
Supplementary files format and content: bwa_counts.txt includes counts for each miRNA across all samples

molecule: other

organism: Mus musculus

source_name: muscle

growth_protocol: C2C12 were cultured in DMEM media with 10% FBS and 1x pen/strep under 37C at 5% CO2.

extract_protocol:
EVs were purified using standard differential centrifugation protocol and sent for miRNA-seq
miRNA-seq

value: muscle

tag: cell line

tag: cell type

value: myoblast

tag: genotype

value: WT

tag: treatment

value: hydrogen peroxide


description:
Library name: V5
V24GW Upper Part Of The right Medulla Oblongata


title: T12GW Right Midbrain

description:
Library name: T1
T12GW Right Midbrain


title: S9GW Medulla Oblongata

description:
Library name: S4
S9GW Medulla Oblongata


title: T12GW Left Midbrain

description:
Library name: T2
T12GW Left Midbrain


title: U33GW Left Upper Pons

description:
Library name: U4
U33GW Left Upper Pons


title: U33GW Left Midbrain

description:
Library name: U2
U33GW Left Midbrain


title: S9GW Left Midbrain

description:
Library name: S2
S9GW Left Midbrain


title: S9GW Pons

description:
Library name: S3
S9GW Pons


title: R11GW Right Midbrain

description:
Library name: R6
R11GW Right Midbrain


title: S9GW Right Midbrain

description:
Library name: S1
S9GW Right Midbrain


title: R11GW Left Midbrain

description:
Library name: R5
R11GW Left Midbrain


title: R11GW Right Pons

description:
Library name: R4
R11GW Right Pons


title: R11GW Right Medulla Oblongata

description:
Library name: R2
R11GW Right Medulla Oblongata


title: R11GW Left Pons

description:
Library name: R3
R11GW Left Pons


title: R11GW Left Medulla Oblongata

description:
Library name: R1
R11GW Left Medulla Oblongata


title: U33GW Right Pons

description:
Library name: U3
U33GW Right Pons


title: N12GW Middle Part Of The Pons

description:
Library name: N4
N12GW Middle Part Of The Pons


title: N12GW Upper Part Of The Pons

description:
Library name: N3
N12GW Upper Part Of The Pons


description:
Library name: M6
M13GW Lower Part Of The Medulla Oblongata


title: M13GW Medulla Oblongata

description:
Library name: M5
M13GW Medulla Oblongata


title: N12GW Left Midbrain

description:
Library name: N2
N12GW Left Midbrain


title: M13GW Lower Part Of The Pons

description:
Library name: M4
M13GW Lower Part Of The Pons


title: N12GW Medulla Oblongata

description:
Library name: N5
N12GW Medulla Oblongata


title: N12GW Right Midbrain

description:
Library name: N1
N12GW Right Midbrain


title: M13GW Upper Part Of The Pons

description:
Library name: M3
M13GW Upper Part Of The Pons


title: M13GW Left Midbrain

description:
Library name: M2
M13GW Left Midbrain


title: L11GW Pons

description:
Library name: L3
L11GW Pons


title: M13GW Right Midbrain

description:
Library name: M1
M13GW Right Midbrain


title: L11GW Medulla Oblongata

description:
Library name: L1
L11GW Medulla Oblongata


description:
Library name: K14
K17GW Lower Part Of The Medulla Oblongata


title: K17GW Right Medulla Oblongata

description:
Library name: K12
K17GW Right Medulla Oblongata


title: K17GW Middle-to-lower Part Of The Pons

description:
Library name: K10
K17GW Middle-to-lower Part Of The Pons


description:
Library name: K11
K17GW Middle Part Of The Medulla Oblongata


title: K17GW Left Upper Part Of The Pons

description:
Library name: K8
K17GW Left Upper Part Of The Pons


title: L11GW Midbrain

description:
Library name: L4
L11GW Midbrain


title: K17GW Central Upper Part Of The Pons

description:
Library name: K6
K17GW Central Upper Part Of The Pons


title: K17GW Right Upper Part Of The Pons

description:
Library name: K7
K17GW Right Upper Part Of The Pons


title: K17GW Lower Left Part Of The Midbrain

description:
Library name: K5
K17GW Lower Left Part Of The Midbrain


title: K17GW Lower right Part Of The Midbrain

description:
Library name: K4
K17GW Lower right Part Of The Midbrain


title: K17GW Right Upper Midbrain

description:
Library name: K2
K17GW Right Upper Midbrain


title: K17GW Left Upper Midbrain

description:
Library name: K1
K17GW Left Upper Midbrain


title: J12GW Right Midbrain

description:
Library name: J5
J12GW Right Midbrain


title: J12GW Left Midbrain

description:
Library name: J4
J12GW Left Midbrain


title: I11GW Pons

description:
Library name: I2
I11GW Pons


title: I11GW Midbrain

description:
Library name: I3
I11GW Midbrain


title: I11GW Medulla Oblongata

description:
Library name: I1
I11GW Medulla Oblongata


description:
Library name: H15
H17GW Central Part Of The Medulla Oblongata


title: J12GW Right Pons

description:
Library name: J3
J12GW Right Pons


title: H17GW Right Medulla Oblongata

description:
Library name: H13
H17GW Right Medulla Oblongata


title: H17GW Lower Middle Part Of Pons

description:
Library name: H11
H17GW Lower Middle Part Of Pons


description:
Library name: K13
K17GW Middle-to-lower Part Of The Medulla Oblongata


title: H17GW Right Lower Pons

description:
Library name: H9
H17GW Right Lower Pons


title: H17GW Right Upper Pons

description:
Library name: H6
H17GW Right Upper Pons


title: H17GW Left Upper Pons

description:
Library name: H8
H17GW Left Upper Pons


title: H17GW Left Lower Pons

description:
Library name: H10
H17GW Left Lower Pons


title: K17GW Right Middle Part Of The Pons

description:
Library name: K9
K17GW Right Middle Part Of The Pons


title: H17GW Middle Of The Left Midbrain

description:
Library name: H4
H17GW Middle Of The Left Midbrain


title: H17GW Left Upper Midbrain

description:
Library name: H2
H17GW Left Upper Midbrain


title: K17GW Middle Part Of The Midbrain

description:
Library name: K3
K17GW Middle Part Of The Midbrain


title: H17GW Right Upper Midbrain

description:
Library name: H1
H17GW Right Upper Midbrain


title: F14GW Right Midbrain

description:
Library name: F2
F14GW Right Midbrain


title: F14GW Left Pons

description:
Library name: F3
F14GW Left Pons


title: J12GW Medulla Oblongata

description:
Library name: J1
J12GW Medulla Oblongata


title: E28GW Right Pons

description:
Library name: E3
E28GW Right Pons


title: F14GW Right Pons

description:
Library name: F1
F14GW Right Pons


title: H17GW Left Medulla Oblongata

description:
Library name: H14
H17GW Left Medulla Oblongata


title: D16GW Left Pons

description:
Library name: D3
D16GW Left Pons


title: D16GW Medulla Oblongata

description:
Library name: D1
D16GW Medulla Oblongata


title: F14GW Left Midbrain

description:
Library name: F4
F14GW Left Midbrain


title: C18GW Midbrain

description:
Library name: C4
C18GW Midbrain


description:
Library name: H7
H17GW Upper Central Part Of The Midbrain


title: E28GW Left Midbrain

description:
Library name: E2
E28GW Left Midbrain


title: C18GW Medulla Oblongata

description:
Library name: C1
C18GW Medulla Oblongata


title: B12GW Right Midbrain

description:
Library name: B6
B12GW Right Midbrain


description:
Library name: H5
H17GW Lower Central Part Of The Midbrain


title: C18GW Right Pons

description:
Library name: C3
C18GW Right Pons


title: B12GW Left Midbrain

description:
Library name: B5
B12GW Left Midbrain


title: E28GW Left Pons

description:
Library name: E1
E28GW Left Pons


title: B12GW Right Pons

description:
Library name: B4
B12GW Right Pons


title: A11GW Left Midbrain

description:
Library name: A6
A11GW Left Midbrain


title: B12GW Left Medulla Oblongata

description:
Library name: B2
B12GW Left Medulla Oblongata


title: A11GW Left Pons

description:
Library name: A4
A11GW Left Pons


title: A11GW Right Pons

description:
Library name: A3
A11GW Right Pons


title: H17GW Middle Of The right Midbrain

description:
Library name: H3
H17GW Middle Of The right Midbrain


title: A11GW Right Medulla Oblongata

description:
Library name: A1
A11GW Right Medulla Oblongata


title: D16GW Right Pons

description:
Library name: D2
D16GW Right Pons


title: KYSE150, GFP-TFAP2β-ΔIDR3, GFP(Input), replicate 1

city: Chengdu

first: Lu

last: Pu

state: Sichuan

address: #37 Guoxue Alley, Wuhou District

institute: west china hospital

description: Library name: KYSE150, GFP-TFAP2β-ΔIDR3, Input, replicate 1

library_source: genomic

data_processing:
The DNA libraries were sequenced on the DNBSEQ-T7 platform.
ChlP-seg reads were trimmed from 3' end until the final base had a quality score > 30.using Trimmomatic v0.33, discarding reads left with < 18 bp
ChlP-seg reads were aligned to the UcSc hg38 genome using Bowtie version 1.1.2Only uniquely mapping reads with at most two mismatches were retained.
To create ChlP-seg coverage plots, the locations of the mapped ChlP-seq reads wereextended to 150 bp to represent sequenced fragments, renormalized (to reads permillion, rpm) and reformatted in the bigWig file format
Peaks were called uing MACS v2.1.0 with the sianificance cut-off a-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score representsthe normalized coverage of DNA fragments at a given genomic coordinate. narrowPeakfiles were generated using MACS v2 with default settings.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: RMPI 1640, 10% fetal bovine serum, 1×penicillin-streptomycin. Cells were cultured at 37 ℃ at 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysischromatin was sonicated using a ultrasonicator.
ChlP-seg libraries were prepared using the SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology, #9003S).

value: esophageal squamous cell carcinoma cell


title: KYSE150, GFP-TFAP2β-ΔIDR3, GFP(ChIP), replicate 1

description: Library name: KYSE150, GFP-TFAP2β-ΔIDR3 , ChIP, replicate 1


title: C18GW Left Pons

description:
Library name: C2
C18GW Left Pons


title: KYSE150, GFP-TFAP2β-ΔIDR3, GFP(ChIP), replicate 2

description: Library name: KYSE150, GFP-TFAP2β-ΔIDR3, ChIP, replicate 2


title: KYSE150, GFP-TFAP2β-Mut_IDR3, GFP(ChIP), replicate 1

description: Library name: KYSE150, GFP-TFAP2β-Mut_IDR3, ChIP, replicate 1


title: KYSE150, GFP-TFAP2β, GFP(ChIP), replicate 2

description: Library name: KYSE150, GFP-TFAP2β, ChIP, replicate 2


title: KYSE150, GFP-TFAP2β-Mut_IDR3, GFP(Input), replicate 1

description: Library name: KYSE150, GFP-TFAP2β-Mut_IDR3, Input, replicate 1


title: KYSE150, GFP-TFAP2β-Mut_IDR3, GFP(Input), replicate 2

description: Library name: KYSE150, GFP-TFAP2β-Mut_IDR3, Input, replicate 2


title: A11GW Left Medulla Oblongata

description:
Library name: A2
A11GW Left Medulla Oblongata


title: KYSE150, GFP-TFAP2β, GFP(Input), replicate 2

description: Library name: KYSE150, GFP-TFAP2β, Input, replicate 2


title: day15_1140T5a_B3_Tr

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

country: France

institute: INRAE

description: Library name: S16250_6_B3_Tr

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
FastQ files were collected and preprocessed with fastp 0.20.1, which enabled UMI preprocessing and polyA trimming. Reads were mapped to the transcriptome reference genome (Ens109, Bos_taurus.ARS-UCD1.2) using TopHat (v2.1.1) and Bowtie2 (v2.3.4.1). As UTR regions are still not well defined in bovine genome, quant3p tool was used to extend annotations in the 3’ end of the transcript.
Assembly: ARS-UCD1.2
Supplementary files format and content: counts_table

molecule: polyA RNA

organism: Bos taurus

source_name: trophectoderm

extract_protocol:
Serie S16250, day-15 trophectoderm : 1 µg of RNA is provided in different volume depending of the RNA concentration. RNA was extracted using Trizol followed by Qiagen column. Concentrations were determined using nanodrop and quality using nanopuce on AgilentX2100 bioanalyzer (reports are available). Serie S17343, day-8 trophectoderm : RNA purified using picopure column (acturus, Thermo). The quantities were not determined because of the very small quantities of material.
Full length cDNA were generated from 4ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Clontech, Part number 634890) according to manufacturerXs instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase (Clontech). Six hundreds ng of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT kit (Illumina, Part number FC-131-1096) followed by 12 cycles of library amplification. Following purification using Agencourt AMPure XP beads (Beckman Coulter, Part number A63882), the size and concentration of library DNA were assessed on an Agilent 2100 Bioanalyzer.

value: trophectoderm

value: trophoblastic cell

value: day-15 conceptus

tag: read length


title: KYSE150, GFP-TFAP2β, GFP(ChIP), replicate 1

description: Library name: KYSE150, GFP-TFAP2β, ChIP, replicate 1


title: day15_1140T6b_B2_Tr

description: Library name: S16250_7_B2_Tr


title: day8_N1P1-36_TE_36

description: Library name: S17343_4_TE_36

value: day-8 embryo


title: day8_N1P1-2_TE_2

description: Library name: S17343_3_TE_2


title: day8_N1P1-4_TE_4

description: Library name: S17343_1_TE_4


title: KYSE150, GFP-TFAP2β, GFP(Input), replicate 1

description: Library name: KYSE150, GFP-TFAP2β, Input, replicate 1


title: day15_1140T1a_B4_Tr

description: Library name: S16250_5_B4_Tr


title: A11GW Right Midbrain

description:
Library name: A5
A11GW Right Midbrain


title: day15_1140T4_B1_Tr

description: Library name: S16250_B1_Tr


title: day15_1138T4a_A7_Tr

description: Library name: S16250_4_A7_Tr


title: KYSE150, GFP-TFAP2β-ΔIDR3, GFP(Input), replicate 2

description: Library name: KYSE150, GFP-TFAP2β-ΔIDR3, Input, replicate 2


title: day15_1138T1_A5_Tr

description: Library name: S16250_A5_Tr


title: KYSE150, GFP-TFAP2β-Mut_IDR3, GFP(ChIP), replicate 2

description: Library name: KYSE150, GFP-TFAP2β-Mut_IDR3, ChIP, replicate 2


title: RNA_shPHF8-3

city: Barcelona

first: Marta

middle: Artés

last: Hernández

address: Baldiri Reixac 15

country: Spain

institute: IBMB-CSIC

description:
Library name: RNA_shPHF8-3
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment. Libraries were prepared using BGI’s standard RNA-seq protocol and sequenced with 20M reads per sample on DNBSEQ PE150

data_processing:
Paired-end analysis Differential expression analysis using DESeq2
Assembly: mm10
Supplementary files format and content: Bed files contain genomic coordinates. BigWig files contain the information for displaying graphs.

source_name: cerebral cortex

growth_protocol: NSCs were cultured in a poly-D-lysine (5 mg/ml, 2 hours at 37°C) and laminin (5 mg/ml, 4 hours at 37°C) pre-coated dishes growing with a media comprising equal parts DMEM F12 (without Phenol Red, Gibco) and Neural Basal Media (Gibco) containing penicillin/streptomycin and Glutamax (1%), N2 and B27 supplements (Gibco), non essential amino acids (0.1 mM), sodium pyruvate (1 mM), Hepes (5 mM), heparin (2 mg/l), bovine serum albumin (25 mg/l) and -mercaptoethanol (0.01 mM). We added fresh recombinant human EGF (R&D Systems) and FGF (Invitrogen) to 20 ng/ml and 10 ng/ml final, respectively.

treatment_protocol: Cells were infected with lentiviral shRNA either scramble (control) or against PHF8 (shPHF8)

value: cerebral cortex

value: neural stem cells

value: PHF8 knockdown

value: lentiviral transduction


title: day8_N1P1-14_TE_14

description: Library name: S17343_2_TE_14


title: RNA_shPHF8-2

description:
Library name: RNA_shPHF8-2
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment. Libraries were prepared using BGI’s standard RNA-seq protocol and sequenced with 20M reads per sample on DNBSEQ PE150


title: RNA_shCTR-2

description:
Library name: RNA_shCTR-2
NSCs were infected with lentiviral shRNA scramble (shCTR). RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment. Libraries were prepared using BGI’s standard RNA-seq protocol and sequenced with 20M reads per sample on DNBSEQ PE150

value: CTR


title: RNA_shPHF8-1

description:
Library name: RNA_shPHF8-1
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment. Libraries were prepared using BGI’s standard RNA-seq protocol and sequenced with 20M reads per sample on DNBSEQ PE150


title: RNA_shCTR-3

description:
Library name: RNA_shCTR-3
NSCs were infected with lentiviral shRNA scramble (shCTR). RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment. Libraries were prepared using BGI’s standard RNA-seq protocol and sequenced with 20M reads per sample on DNBSEQ PE150


title: RNA_shCTR-1

description:
Library name: RNA_shCTR-1
NSCs were infected with lentiviral shRNA scramble (shCTR). RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment. Libraries were prepared using BGI’s standard RNA-seq protocol and sequenced with 20M reads per sample on DNBSEQ PE150


title: ChIPseq_H3K9me3_shPHF8_input

description:
Library name: shPHF8_input
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)

data_processing:
Single-end reads were aligned to the mouse mm10 reference genome using Bowtie2 (v2.3.5.1) with default options. SAMtools (v1.9) was used to filter out the low-quality alignments using the flag 3844. The resulting BAM files were sorted and deepTools was used to generate input-subtracted and counts per million (CPM) normalized signal tracks (bamCompare -- operation subtract -- normalizeUsing CPM --scaleFactorsMethod None) in bigWig format.
Assembly: mm10
Supplementary files format and content: bigWig files include input-subtracted ChIP-Seq signal.

extract_protocol:
1x 10^6NSCs were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.
The libraries were prepared and amplified to make DNA NanoBall (DNB) Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: ChIPseq_H3K9me3_shPHF8_rep1

description:
Library name: shPHF8-R1
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: ChIPseq_H3K9me3_shPHF8_rep2

description:
Library name: shPHF8-R2
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: ChIPseq_H3K9me3_shCTR_input

description:
Library name: shCTR_input
NSCs were infected with lentiviral shRNA scramble (shCTR). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: 212_count

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Library name: 212_count

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference via bowtie2, done by BGI (Shenzhen, China)
sRNA classification dony by BGI (Shenzhen, China)
Assembly: mm10
Supplementary files format and content: file containing small RNA counts for each sample

source_name: Gonadal white adipise tissue

extract_protocol:
total RNA was extracted using a miRNeasy kit (Qiagen, Germany) as per the manufacturer’s instructions
done by BGI (Shenzhen, China)

value: Gonadal white adipise tissue

tag: strain

value: NZO/HIBomDife

tag: Sex

value: Female

tag: disease state

value: diabetes-resistant


title: 211_count

description: Library name: 211_count


title: 210_count

description: Library name: 210_count

value: diabetes-prone


title: 209_count

description: Library name: 209_count


title: ChIPseq_H3K9me3_shCTR_rep2

description:
Library name: shCTR-R2
NSCs were infected with lentiviral shRNA scramble (shCTR). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: 208_count

description: Library name: 208_count


title: B12GW Left Pons

description:
Library name: B3
B12GW Left Pons

value: brainstem


title: 207_count

description: Library name: 207_count


title: 206_count

description: Library name: 206_count


title: 205_count

description: Library name: 205_count


title: day15_1138T3a_A8_Tr

description: Library name: S16250_3_A8_Tr


title: 204_count

description: Library name: 204_count


title: 203_count

description: Library name: 203_count


title: 200_count

description: Library name: 200_count


title: 202_count

description: Library name: 202_count


title: 201_count

description: Library name: 201_count


title: 198_count

description: Library name: 198_count


title: 197_count

description: Library name: 197_count


title: 199_count

description: Library name: 199_count


title: 193_count

description: Library name: 193_count


title: 192_count

description: Library name: 192_count


title: 191_count

description: Library name: 191_count


title: 195_count

description: Library name: 195_count


title: 194_count

description: Library name: 194_count


title: 188_count

description: Library name: 188_count


title: 190_count

description: Library name: 190_count


title: 187_count

description: Library name: 187_count


title: 186_count

description: Library name: 186_count


title: ChIPseq_H3K9me3_shCTR_rep1

description:
Library name: shCTR-R1
NSCs were infected with lentiviral shRNA scramble (shCTR). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: 183_count

description: Library name: 183_count


title: 189_count

description: Library name: 189_count


title: 185_count

description: Library name: 185_count


title: 211

description: Library name: 211

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.4a
calling done with STRINGTIE v2.1.3b
Assembly: GRCm38.p6
Supplementary files format and content: file containing gene counts for each sample


title: 184_count

description: Library name: 184_count


title: 210

description: Library name: 210


title: 207

description: Library name: 207


title: 204

description: Library name: 204


title: 206

description: Library name: 206


title: 208

description: Library name: 208


title: 205

description: Library name: 205


title: 202

description: Library name: 202


title: 201

description: Library name: 201


title: 199

description: Library name: 199


title: 197

description: Library name: 197


title: 195

description: Library name: 195


title: 196

description: Library name: 196


title: 193

description: Library name: 193


title: 194

description: Library name: 194


title: 200

description: Library name: 200


title: 212

description: Library name: 212


title: 191

description: Library name: 191


title: 192

description: Library name: 192


title: 190

description: Library name: 190


title: 189

description: Library name: 189


title: 188

description: Library name: 188


title: 209

description: Library name: 209


title: 184

description: Library name: 184


title: 183

description: Library name: 183


title: ChIPseq_shPHF8_input

description:
Library name: shPHF8_input.fq
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)

data_processing:
For RNA-seq, alignment was performed using HISAT2. Assignment of aligned reads to genes using HTSeq.Differential expression analysis using DESeq2
For ChIP-seq, single-end reads were aligned to the mouse mm10 reference genome using Bowtie2 (v2.3.5.1) with default options. SAMtools (v1.9) was used to filter out the low-quality alignments using the flag 3844. The resulting BAM files were sorted and deepTools was used to generate input-subtracted and counts per million (CPM) normalized signal tracks (bamCompare -- operation subtract -- normalizeUsing CPM --scaleFactorsMethod None) in bigWig format.
For ATAC-seq, paired-end reads were aligned to the mouse mm10 reference genome using Bowtie2 (v2.3.5.1) and specifying the "--very-sensitive-local" mode. SAMtools (v1.9) was used to filter out the low-quality reads with the flag 1796, remove reads mapped in the mitochondrial chromosome, and discard those with a MAPQ score below 20. The resulting BAM files were sorted and deepTools was used to generate counts per million (CPM) normalized signal tracks (bamCoverage --samFlagInclude 64 --normalizeUsing CPM) in bigWig format. The peak calling was performed with MACS2 (v.2.1.2) by specifying the -BAMPEmode.
Assembly: mm10
Supplementary files format and content: Bed files contain genomic coordinates. BigWig files contain the information for displaying graphs.

extract_protocol:
For RNA-seq, RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment.
For ChIP-seq, NSCs were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.
For ATAC-seq, cells were scrapped and resuspended in RBS buffer and then Igepal CA-630 0.1% was added to achieve cell lysis. Transposition reaction with Transposes enzyme and buffer kits (Illumina, FC-121-1030) and immediately following transposition, DNA was purified.
For RNA-seq, libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Human/Mouse/Rat Kit (ref. RS-122-2201/2, Illumina) according to the manufacturer's protocol. Briefly, 500 ng of total RNA was used for ribosomal RNA depletion RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina High HiSeq 2500)
For ChIP-seq, the libraries were prepared and amplified to make DNA NanoBall (DNB). Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)
For ATAC-seq, Nextera DNA Library Prep Kit (FC-121-1030), along with unique dual index barcodes for each sample and NEBNext High-Fidelity 2x PCR Master Mix (New England Lab, M0541) were used. Ampure XP beads (Beckman Coulter, A63880) were prepared for size selection. Libraries were then pair-end sequenced using NextSeq2000 and approximately 50M reads per sample were obtained.


title: ChIPseq_shPHF8_rep2

description:
Library name: shPHF8_2.fq
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: 203

description: Library name: 203


title: ChIPseq_shPHF8_rep1

description:
Library name: shPHF8_1.fq
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: ChIPseq_shCTR_rep1

description:
Library name: shCTR_1.fq
NSCs were infected with lentiviral shRNA scramble (shCTR). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: ChIPseq_shCTR_input

description:
Library name: shCTR_input.fq
NSCs were infected with lentiviral shRNA scramble (shCTR). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: ChIPseq_shCTR_rep2

description:
Library name: shCTR_2.fq
NSCs were infected with lentiviral shRNA scramble (shCTR). Cells were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.The libraries were prepared and amplified to make DNA NanoBall (DNB)Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)


title: bulk, stimulated, M3, RNA

city: Iowa City

first: Muhammad

last: Elsadany

state: IA

address: 25 S Grand Ave

department: Psychiatry

country: USA

institute: University of Iowa

description: Library name: bulk_M3B_RNA

data_processing:
Bulk RNA-seq raw files were processed with bcbio-nextgen-1.2.9. Multiomic raw files were processed with cellranger-arc-2.0.2 and used as input to build a Seurat object in R. Cell type labeling was done by integration with the Allen Institute dataset. pseudo-bulk was done by sampling random cells and aggregating them per cell type.
Assembly: hg38 for human samples and mm10 for mouse data
Supplementary files format and content: RDS file for the Seurat object of each sample. the object contains RNA gene expression, Gene activity from ATAC, and metadata containing cell type labeling and other meta information. no filtering was done for this file and it contains the output from CellRanger arc: E1A.rds, E1B.rds, E2A.rds, E2B.rds, E3A.rds, E3B.rds, E4A.rds, E4B.rds, G1A.rds, G1B.rds, G2A.rds, G2B.rds another separate RDS file for each sample is provided for the pseudo-bulk RNA data per cell type. txt files for bulk RNA-Seq data from stimulated and unstimulated paradigms from human and mouse: each column is for a different sample and includes the raw counts per transcript.

source_name: non-primary auditory

extract_protocol:
for bulk RNA-Seq, total RNA was extracted using miRNeasy Mini Kite and homogenized in Qiazol using stainless steel beads. Chloroform was then used for phase separation. RNA containing an aqueous layer was further purified using the RNeasy MinElute spin column. RNA was finally eluted in RNase-free water. for sn-multi-omics, nuclei were isolated using the Chromium Nuclei Isolation Kit. Nuclei were directly processed for droplet capture for single cell multiome ATAC + gene expression using a chromium controller.
For bulk RNA-seq, librairies were prepared using Ribo-Zero gold sample preparation kit. Library concentrations were measured using KAPA Illumina Library Quantification Kit. Pooled libraries were sequenced on Illumina NovaSeq6000 sequencer with 150-bp Paired-End chemistry. For sn-multi-omics, Chromium Next GEM Single Cell Multiome ATAC + Gene v1 chemistry was used to create single nuclei ATAC and RNA libraries from the same cell. Libraries were sequenced on an Illumina Novaseq 6000 with a 150 bp paired end read setup.

value: non-primary auditory

tag: hemisphere

value: left

tag: condition

value: stimulated

value: neurons/glia

value: M

tag: age

tag: anesthesia

value: isoflurane:5% induction and 2% maintainance

tag: paradigm


title: bulk, stimulated, M4, RNA

description: Library name: bulk_M4B_RNA

value: right


title: bulk, baseline, M4, RNA

description: Library name: bulk_M4A_RNA

value: baseline


title: bulk, baseline, M3, RNA

description: Library name: bulk_M3A_RNA


title: bulk, baseline, M2, RNA

description: Library name: bulk_M2A_RNA


title: bulk, baseline, M1, RNA

description: Library name: bulk_M1A_RNA


title: bulk, stimulated, M1, RNA

description: Library name: bulk_M1B_RNA


title: 187

description: Library name: 187


title: 185

description: Library name: 185


title: 186

description: Library name: 186


title: PCLS-EV, Young Uninjured, Rep 3

city: London

first: Sally

middle: Yunsun

last: Kim

address: Franklin-Wilkins Building, 150 Stamford Street

department: Institute of Pharmaceutical Sciences

institute: King's College London

description: Library name: Young_Control_EV_2201216

data_processing:
The sequencing libraries generated contain unique molecular index (UMI) sequences, which are used to ensure that only unique molecules are used for subsequent analysis. This is done by collapsing identical UMI containing sequence reads. FASTX-Toolkit was used to quality-filter reads and cutadapt was used to remove adaptor sequences. Fastqc and MultiQC was used to ensure high quality sequencing data. Filtered reads were mapped using Bowtie to a list of datasets. First, reads were mapped to tRNA sequences from Genomic tRNA Database (GtRNAdb). Unmapped reads were then mapped to miRNAs from miRBase v22 allowing zero mismatches, but allowing for non-templated 3’ A and T bases. Unmapped reads were the mapped against other relevant small RNA datasets: piRNA, tRNA, snRNA, snoRNA and Y RNA allowing one mismatch. The remaining unmapped reads were mapped to rRNA datasets. This was done to discover which RNA species were present in the sequencing data. The miRNA RNA expression profiles generated were used for differential expression analysis in R using the DESeq2 package.
Assembly: miRBase version 22
Supplementary files format and content: TXT file includes raw counts for each sample

source_name: Lung

growth_protocol: PCLS were obtained from lungs of young adult (aged 10–12 weeks) or aged (aged > 18 months) C57BL/6J mice and cultured in serum-free DMEM (Sigma, 31966-201) with 1% penicillin-streptomycin (Merck, P0781) for 48 hours.

extract_protocol:
PCLS-EVs were isolated using size exclusion chromatography (IZON, ICO-35) from media used to culture 30 PCLS for each physiological condition. Total RNA was extracted from EVs with Direct-zolTM RNA Microprep kit (Zymo Research, R2060).
RNA was prepared for small RNA sequencing using the QIAseq miRNA Library Kit (Qiagen). Quality control of the libraries was performed using the Bioanalyzer 2100 High Sensitivity DNA Assay (Agilent) and quantified using the Qubit dsDNA HS (High Sensitivity) Assay Kit (Thermo Fisher)

treatment_protocol: Young and aged PCLS were either injured with 0.1M HCl acid or left uninjured prior to culture.

value: Lung

value: 10–12 wks

value: WT


title: PCLS-EV, Young Uninjured, Rep 1

description: Library name: Young_Control_EV_220609


title: PCLS-EV, Young Injured, Rep 2

description: Library name: Young_Injured_EV_220610


title: PCLS-EV, Young Injured, Rep 1

description: Library name: Young_Injured_EV_220609


title: PCLS-EV, Aged Injured, Rep 3

description: Library name: Aged_Injured_EV_2207134

value: > 18 months


title: PCLS-EV, Young Uninjured, Rep 2

description: Library name: Young_Control_EV_220610


title: PCLS-EV, Young Injured, Rep 3

description: Library name: Young_Injured_EV_2201218


title: PCLS-EV, Aged Injured, Rep 1

description: Library name: Aged_Injured_EV_220609


title: PCLS-EV, Aged Injured, Rep 2

description: Library name: Aged_Injured_EV_2207132


title: PCLS-EV, Aged Uninjured, Rep 2

description: Library name: Aged_Control_EV_2207131


title: PCLS-EV, Aged Uninjured, Rep 3

description: Library name: Aged_Control_EV_2207133


title: PCLS-EV, Aged Uninjured, Rep 1

description: Library name: Aged_Control_EV_220609


title: bulk, stimulated, M2, RNA

description: Library name: bulk_M2B_RNA


title: L0-37649_2, 262, CCI_GR_2

city: Bethesda

first: Martin

middle: L

last: Doughty

state: MD

address: 4301 Jones Bridge Road

department: APG

institute: USU

description:
Library name: L0-37649_2
Fresh frozen Spatial transcriptome sequencing

data_processing:
We deployed 10X Genomics Space Ranger 1.3.1 with resultant FASTQs and H&E tissue histology TIFF images to perform automatic slide image processing, read alignment, and spatial barcode/UMI counting. Reads were aligned to the Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6).
Assembly: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary files format and content: Processed data files include tissue section images and spaceranger output.
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
Brain tissue preparation was performed following Visium Spatial Protocols – Tissue Preparation Guide (Document number CG000240, Rev C, 10X Genomics)
Generation of spatial transcriptomic data was performed following the fresh frozen Visium Spatial GEX User Guide (Document number CG000239, Rev E, 10X Genomics)

value: brain

tag: sample id_#

value: C57BL/6J wild-type

tag: timepoint post-injury

value: CCI

value: GR


title: L0-37647_2, 264, CCI_GR_2

description:
Library name: L0-37647_2
Fresh frozen Spatial transcriptome sequencing


title: L0-37646_2, 263, CCI_GR_2

description:
Library name: L0-37646_2
Fresh frozen Spatial transcriptome sequencing


title: L0-37644_2, 247, CCI_Ctrl_2

description:
Library name: L0-37644_2
Fresh frozen Spatial transcriptome sequencing

value: Ctrl


title: L0-37648_2, 266, CCI_GR_2

description:
Library name: L0-37648_2
Fresh frozen Spatial transcriptome sequencing


title: L0-37650_1, 211, CCI_Ctrl_7

description:
Library name: L0-37650_1
Fresh frozen Spatial transcriptome sequencing


title: L0-37640, 237, CCI_GR_7

description:
Library name: L0-37640
Fresh frozen Spatial transcriptome sequencing


title: L0-37641, 239, CCI_GR_7

description:
Library name: L0-37641
Fresh frozen Spatial transcriptome sequencing


title: L0-37635, 236, CCI_GR_7

description:
Library name: L0-37635
Fresh frozen Spatial transcriptome sequencing


title: L0-37636, 245, CCI_Ctrl_7

description:
Library name: L0-37636
Fresh frozen Spatial transcriptome sequencing


title: L0-37645_2, 256, CCI_GR_2

description:
Library name: L0-37645_2
Fresh frozen Spatial transcriptome sequencing


title: L0-37643_2, 249, CCI_Ctrl_2

description:
Library name: L0-37643_2
Fresh frozen Spatial transcriptome sequencing


title: L0-37642_2, 248, CCI_Ctrl_2

description:
Library name: L0-37642_2
Fresh frozen Spatial transcriptome sequencing


title: L0-37637, 244, CCI_Ctrl_7

description:
Library name: L0-37637
Fresh frozen Spatial transcriptome sequencing


title: L0-33047, 183, Sham_None_2

description:
Library name: L0-33047
Fresh frozen Spatial transcriptome sequencing

value: Sham


title: L0-37639, 243_2, CCI_Ctrl_7

description:
Library name: L0-37639
Fresh frozen Spatial transcriptome sequencing


title: L0-33046, 182, Sham_None_2

description:
Library name: L0-33046
Fresh frozen Spatial transcriptome sequencing


title: L0-37634, 235, CCI_GR_7

description:
Library name: L0-37634
Fresh frozen Spatial transcriptome sequencing


title: L0-34632_3, 224, CCI_GR_7

description:
Library name: L0-34632_3
Fresh frozen Spatial transcriptome sequencing


title: L0-34637_2, 225, CCI_GR_7

description:
Library name: L0-34637_2
Fresh frozen Spatial transcriptome sequencing


title: L0-34636_2, 213, CCI_Ctrl_7

description:
Library name: L0-34636_2
Fresh frozen Spatial transcriptome sequencing


title: L0-34633_2, 223, CCI_GR_7

description:
Library name: L0-34633_2
Fresh frozen Spatial transcriptome sequencing


title: L0-33045, 176, CCI_None_2

description:
Library name: L0-33045
Fresh frozen Spatial transcriptome sequencing


title: L0-33044, 181, CCI_None_2

description:
Library name: L0-33044
Fresh frozen Spatial transcriptome sequencing


title: L0-29201, 140, CCI_None_7

description:
Library name: L0-29201
Fresh frozen Spatial transcriptome sequencing


title: L0-29202, 141, Sham_None_7

description:
Library name: L0-29202
Fresh frozen Spatial transcriptome sequencing


title: L0-33042, 184, Sham_None_2

description:
Library name: L0-33042
Fresh frozen Spatial transcriptome sequencing


title: L0-29197, 147, CCI_None_7

description:
Library name: L0-29197
Fresh frozen Spatial transcriptome sequencing


title: L0-29196, 149, CCI_None_7

description:
Library name: L0-29196
Fresh frozen Spatial transcriptome sequencing


title: L0-29203, 143, Sham_None_7

description:
Library name: L0-29203
Fresh frozen Spatial transcriptome sequencing


title: L0-29199, 142, CCI_None_7

description:
Library name: L0-29199
Fresh frozen Spatial transcriptome sequencing


title: L0-29198, 150, Sham_None_7

description:
Library name: L0-29198
Fresh frozen Spatial transcriptome sequencing


title: L0-34635_1, 206, CCI_Ctrl_2

description:
Library name: L0-34635_1
Fresh frozen Spatial transcriptome sequencing


title: #58 5xFAD hippocampus, Aducanumab treatment

city: Nanjing

first: Guangyu

last: Long

state: Jiangsu

address: #639 longmian avenue

institute: China Pharmaceutical University

description: Library name: Adu58

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: Ensembl_v112
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: hippocampus

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: hippocampus

value: Aducanumab


title: #55 5xFAD hippocampus, ACLP-NT treatment

description: Library name: Z55

value: ACLP-NT


title: #38 5xFAD hippocampus, saline treatment

description: Library name: AD38

value: saline


title: #53 5xFAD hippocampus, ACLP-NT treatment

description: Library name: Z53


title: #49 5xFAD hippocampus, ACLP-NT treatment

description: Library name: Z49


title: #50 5xFAD hippocampus, Aducanumab treatment

description: Library name: Adu50


title: L0-33043, 177, CCI_None_2

description:
Library name: L0-33043
Fresh frozen Spatial transcriptome sequencing


title: #19 5xFAD hippocampus, saline treatment

description: Library name: AD19


title: #56 5xFAD hippocampus, Aducanumab treatment

description: Library name: Adu56


title: #32 5xFAD hippocampus, saline treatment

description: Library name: AD32


title: #27 5xFAD hippocampus, ACLP-NT treatment

description: Library name: Z27


title: Dex1

city: Boston

first: Judith

last: Agudo

state: MA

address: 1 Jimmy fund way

institute: Dana Farber Cancer Institute

description: Library name: Dex1

data_processing:
Reads were filtered for quality and adapters were removed using TrimGalore (v0.6.10). Filtered reads were aligned to GRCM39 or the E.coli genome using bowtie2 (v2.5.4).
MACS3 (v3.0.3) was used to call peaks with significance cutoff q<0.01.
Bam files were scaled to 10 million reads in 1bp bins (bamcoverage --scaleFactor -bs 1 --effectiveGenomeSize 2654621783 –exactScaling) and replicates were averaged using bigwigAverage(-bs 1). Resulting bigWig files are provided.
Assembly: Mouse GRCM39
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed using the EpiCypher (V4) kit according to manufacturer instructions from 500,000 cells. Permeabilization was performed using 0.01% Digitonin and 0.5ug of Glucocorticoid Receptor antibody (CST #12041) was used for overnight immunoprecipitation. E.Coli Spike-in DNA was added after chromatin digestion.
Resulting DNA was submitted to GENEWIZ for library construction and sequencing using Nova-Seq 2x150bp chemistry.

treatment_protocol: 4T1 tumour cells were treated with Dexamethasone (700 nM) or vehicle control for 7 days in vitro and cells were collected from culture by Trypsin detachment following standard procedure.

value: Dexamethasone

tag: chip antibody


title: Control2

description: Library name: Control2

value: Vehicle control

value: Glucocorticoid Receptor antibody (CST #12041)


title: Control1

description: Library name: Control1


title: #18 5xFAD hippocampus, saline treatment

description: Library name: AD18

tag: tissue


title: 100LL-Lung-D19-NSG

description: Library name: 29---100LL-Lung-D19-NSG

data_processing:
GENEWIZ performed basic computational analysis for quality controls and constructed the gene matrices. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Raw counts are provided.
Gene matrices were normalized using TPM counts by GENEWIZ
Assembly: mm10
Supplementary files format and content: Gene count matrix with genes organized in rows and identified by official gene symbol and samples organized in columns. Provided as raw counts and normalized TPM.

growth_protocol: 4T1-tdTomato tumour cells were injected into BALB/c or NSG female mice. Cells were implanted in the mammary fat pad for primary tumour isolation (200,000 cells) or injected via tail vein (500,000 cells) for isolation from the lung.

extract_protocol:
RNA was extracted with miRNeasy Micro kit (QIAGEN) following the manufacturer’s instructions.
RNA samples were submitted to GENEWIZ for bulk RNA-sequencing. GENEWIZ performed basic computational analysis.

treatment_protocol: Lungs and tumours were digested in 400U/mL Collagenase IV, 20μg/mL DNase I, 10μM Y-27632 compound, 10% FBS in HBSS. Samples were digested for 30 min at 37°C and passed through a 100μm cell strainer followed by RBC lysis. Cells were stained with CD45 and resuspended in 1mL flow buffer with DAPI (1:10,000) for sorting using an AriaIII (BD). Cells were sorted as single cells/DAPI-/CD45-/tdTomato+.

tag: cell line

tag: mouse strain_origin

value: NSG

value: Lung

tag: timepoint/disease stage

value: Macro-met (endpoint)


title: #17 5xFAD hippocampus, ACLP-NT treatment

description: Library name: Z17

tag: treatment


title: 58NN-Lung-D21-Balbc

description: Library name: 24---58NN-Lung-D21-Balbc

value: BALB/c


title: 98L-Lung-D19-NSG

description: Library name: 26---98L-Lung-D19-NSG


title: 57NN-Lung-D23-Balbc

description: Library name: 25---57NN-Lung-D23-Balbc


title: 100R-Lung-D20-NSG

description: Library name: 30---100R-Lung-D20-NSG


title: 98LR-Lung-D19-NSG

description: Library name: 28---98LR-Lung-D19-NSG


title: 98LL-Lung-D19-NSG

description: Library name: 27---98LL-Lung-D19-NSG


title: #24 5xFAD hippocampus, Aducanumab treatment

description: Library name: Adu24


title: 57LR-Lung-D21-Balbc

description: Library name: 23---57LR-Lung-D21-Balbc


title: 58LR-Lung-D21-Balbc

description: Library name: 21---58LR-Lung-D21-Balbc


title: 34RR-Lung-D7-NSG

description: Library name: 20---34RR-Lung-D7-NSG

value: DTC (D7)


title: 35NN-Lung-D7-NSG

description: Library name: 19---35NN-Lung-D7-NSG


title: 35LR-Lung-D7-NSG

description: Library name: 18---35LR-Lung-D7-NSG


title: 25LR-Lung-D7-Balbc

description: Library name: 15---25LR-Lung-D7-Balbc


title: 57L-Lung-D21-Balbc

description: Library name: 22---57L-Lung-D21-Balbc


title: 35L-Lung-D7-NSG

description: Library name: 16---35L-Lung-D7-NSG


title: 25LL-Lung-D7-Balbc

description: Library name: 13---25LL-Lung-D7-Balbc


title: 25L-Lung-D7-Balbc

description: Library name: 11---25L-Lung-D7-Balbc


title: 25NN-Lung-D7-Balbc

description: Library name: 14---25NN-Lung-D7-Balbc


title: Dex2

description: Library name: Dex2


title: 36LR-Tumor-D10-NSG

description: Library name: 9---36LR-Tumor-D10-NSG

source_name: Mammary tumour

value: Mammary tumour

value: Tumour (D10)


title: 36NN-Tumor-D10-NSG

description: Library name: 10---36NN-Tumor-D10-NSG


title: 36LL-Tumor-D10-NSG

description: Library name: 8---36LL-Tumor-D10-NSG


title: 36L-Tumor-D10-NSG

description: Library name: 6---36L-Tumor-D10-NSG


title: 25R-Lung-D7-Balbc

description: Library name: 12---25R-Lung-D7-Balbc


title: 36R-Tumor-D10-NSG

description: Library name: 7---36R-Tumor-D10-NSG


title: 9LL-Tumor-D22-Balbc

description: Library name: 5---9LL-Tumor-D22-Balbc

value: Tumour (D21/22)


title: 9L-Tumor-D22-Balbc

description: Library name: 3---9L-Tumor-D22-Balbc


title: 9R-Tumor-D22-Balbc

description: Library name: 4---9R-Tumor-D22-Balbc


title: Thy1.1_Pool129-2_14

description:
Library name: Thy1.1_Pool129-2_14
10x genomics

library_source: transcriptomic single cell

data_processing:
Reads were mapped to the mouse reference genome (assembly mm10; configured to include introns) and quantified using CellRanger (v8.0.1). Further analyses were performed on filtered count matrices in RStudio (v4.3.2) with the Bioconductor SingleCellExperiment (v1.24.0) framework.
Assembly: Mouse mm10
Supplementary files format and content: Matrix files containing filtered features

growth_protocol: A mix of 4T1-GFP and 4T1-Thy1.1 tumour cells were injected into BALB/c female mice. Pre-activated Jedi CD8+ T cells were adoptively transferred one day prior (25,000 T cells per mouse). Tumour cells were injected via tail vein (500,000 GFP cells; 25,000 Thy1.1 cells per mouse). GFP and Thy1.1 tumour cells were isolated from the same lungs 7 days later.

extract_protocol:
Cells were FACS-sorted on AriaIII (BD) as single cells/DAPI-/CD45-/GFP+ or Thy1.1+. GFP and Thy1.1 samples from different lungs were pooled after sorting for sequencing. Sorted cells were washed and resuspended in PBS+0.04% BSA (400 µg/ml) buffer at cell concentration of 1000 cells/µL.
Libraries were prepared using the 3' v3.1 HT kit from 10x Genomics following manufacturer’s instructions with 10,000 cell recovery and sequenced at 50,000 reads/cell.

treatment_protocol: Lungs were digested in 400U/mL Collagenase IV, 20μg/mL DNase I, 10μM Y-27632 compound, 10% FBS in HBSS. Samples were digested for 30 min at 37°C and passed through a 100μm cell strainer followed by RBC lysis. Cells were stained with CD45 and Thy1.1 antibodies and resuspended in 1mL flow buffer with DAPI (1:10,000) for sorting using an AriaIII (BD).

value: BALB/c with Jedi T cell adoptive transfer


title: 8R-Tumor-D21-Balbc

description: Library name: 2---8R-Tumor-D21-Balbc


title: GFP_Pool129-2_13

description:
Library name: GFP_Pool129-2_13
10x genomics


title: 8L-Tumor-D21-Balbc

description: Library name: 1---8L-Tumor-D21-Balbc


title: shGR_zsGreen_Pool165_28

description:
Library name: shGR_zsGreen_Pool165_28
10x genomics

growth_protocol: 4T1-shGR (Glucocorticoid Receptor, GR, knockdown) and 4T1-shControl breast tumour cells were transduced to express tdTomato and secreted lipid-soluble cTAT-zsGreen. Tumour cells (4T1-tdTomato-cTAT-zsGreen with -shControl or -shGR) were injected into primary tumour-bearing BALB/c mice (500,000 cells per mouse). Tumour cells and labelled niche cells were FACS-sorted from the lungs of mice at D7 post-injection.

extract_protocol:
Cells were FACS-sorted on an AriaIII (BD). Tumour cells were sorted as single cells/DAPI-/CD45-/tdTomato+. Niche cells were sorted as single cells/DAPI-/CD45+, then as CD3/CD8/CD49b+ (all 3 stained in same channel). Samples from different lungs were pooled after sorting for sequencing. Sorted cells were washed and resuspended in PBS+0.04% BSA (400 µg/ml) buffer at cell concentration of 1000 cells/µL.
Libraries were prepared using the 3' v3.1 HT kit from 10x Genomics following manufacturer’s instructions with 10,000 cell recovery and sequenced at 50,000 reads/cell.

treatment_protocol: Lungs were digested in 400U/mL Collagenase IV, 20μg/mL DNase I, 10μM Y-27632 compound, 10% FBS in HBSS. Samples were digested for 30 min at 37°C and passed through a 100μm cell strainer followed by RBC lysis. Cells were stained with CD45, CD3, CD8, CD49b antibodies and resuspended in 1mL flow buffer with DAPI (1:10,000) for sorting using an AriaIII (BD).

tag: cell type

value: Niche (zsGreen+)

value: Tumour-bearing BALB/c


title: shGR_tdTomato_Pool165_27

description:
Library name: shGR_tdTomato_Pool165_27
10x genomics

value: Tumour (tdTomato+)


title: 35LL-Lung-D7-NSG

description: Library name: 17---35LL-Lung-D7-NSG


title: shControl_tdTomato_Pool165_25

description:
Library name: shControl_tdTomato_Pool165_25
10x genomics


title: shControl_zsGreen_Pool165_26

description:
Library name: shControl_zsGreen_Pool165_26
10x genomics


title: NSG2GFP

description: Library name: NSG2GFP

data_processing:
GENEWIZ performed basic computational analysis for quality controls and constructed the gene matrices. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Raw counts are provided.
Assembly: mm10
Supplementary files format and content: Gene count matrix with genes organized in rows and identified by official gene symbol and samples organized in columns.

growth_protocol: 4T1-GFP tumour cells were injected into Jedi or NSG female mice. Cells were injected via tail vein (500,000 cells) for isolation from the lung 7 days later.

extract_protocol:
RNA was extracted with miRNeasy Micro kit (QIAGEN) following the manufacturer’s instructions or by GENEWIZ company using their low input RNA protocol.
RNA samples were submitted to GENEWIZ for low-input bulk RNA-sequencing. GENEWIZ performed basic computational analysis.

treatment_protocol: Lungs were digested in 400U/mL Collagenase IV, 20μg/mL DNase I, 10μM Y-27632 compound, 10% FBS in HBSS. Samples were digested for 30 min at 37°C and passed through a 100μm cell strainer followed by RBC lysis. Cells were resuspended in 1mL flow buffer with DAPI (1:10,000) for sorting using an AriaIII (BD). Cells were sorted as single cells/DAPI-/GFP+.


title: NSG1GFP

description: Library name: NSG1GFP


title: JediLRGFP

description: Library name: JediLRGFP

value: Jedi


title: Jedi4GFP

description: Library name: Jedi4GFP


title: NSG3GFP

description: Library name: NSG3GFP


title: Day 28,Male,Replicate 3

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

description: Library name: D28_M3

data_processing:
Raw base call (BCL) files were converted to FASTQ using Illumina bcl2fastq
Cellranger version 9.0.0 was used to generate sample_raw_feature_bc_matrix output for each sample
Assembly: Mus musculus GRCm39 (Ensembl release 109)
Supplementary files format and content: raw feature bc matrix files consisting barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz are provided for each sample

source_name: Heart

growth_protocol: Male and female C57BL/6J mice (15–20 weeks old) were maintained under standard housing conditions with ad libitum access to food and water.

extract_protocol:
Approximately 50 mg of snap-frozen cardiac tissue was processed using either the 10x Genomics Nuclei Isolation Kit (RNA samples) or the 10x Genomics Sample Fixation and Preparation Kit with Miltenyi OctoMACS dissociation. Nuclei or fixed cell suspensions were assessed with AO/PI on the LunaFx7 automated cell counter for quality and debris content.
Libraries were prepared using 10x Genomics Chromium chemistry

treatment_protocol: Mice were subjected to non-reperfused myocardial infarction (MI) by permanent coronary ligation and harvested at 1, 4, 7, or 28 days post-MI. Day 0 samples represent uninjured controls.

value: Heart

tag: genotype

value: MI Day 28


title: FNP-antiHER2-3

city: tinajin

first: qiqi

last: liu

state: other

address: nankai university

institute: nankai university

description: Library name: FNP-antiHER2-3

data_processing:
Raw data of fastq format were firstly processed through fastp software. In this step, clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The raw RNA-seq reads were aligned to the mouse genome (GRCm38) by HISAT2 (v2.1.0).
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: The read counts for each gene were obtained and normalized as fragments per kilobase of exon model per million mapped fragments (FPKM) mapped fragments.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Tumour cells were treated with FNP-antiHER2 for 24 h.

value: tumour


title: Day 28,Male,Replicate 2

description: Library name: D28_M2


title: CTL-3

description: Library name: Ctrl-3


title: CTL-2

description: Library name: Ctrl-2


title: FNP-antiHER2-2

description: Library name: FNP-antiHER2-2


title: CTL-1

description: Library name: Ctrl-1


title: FNP-antiHER2-1

description: Library name: FNP-antiHER2-1


title: Day 28,Male,Replicate 1

description: Library name: D28_M1


title: Day 28,Female,Replicate 3

description: Library name: D28_F3


title: Day 28,Female,Replicate 2

description: Library name: D28_F2


title: Day 7,Male,Replicate 3

description: Library name: D7_M3

value: MI Day 7


title: Day 7,Male,Replicate 2

description: Library name: D7_M2


title: E. coli infected by P+ phage at low MOI, 10min, rep1

city: Urbana

first: Ido

last: Golding

state: IL

address: 1110 W Green St.

department: Physics

institute: University of Illinois Urbana-Champaign

description: Library name: SA4

data_processing:
FASTQ files for each sample were mapped to the genome using BWA (v0.7.17)
BEDTools (v2.28.0) was used to calculate per-base read depth across the phage genome and per-gene read counts across the E. coli genome.
Assembly: E. coli MG1655 reference genome (NCBI accession: U00096.3) and the phage lambda genome (NCBI accession: NC_001416)
Supplementary files format and content: Raw read counts for E. coli genes are provided in a .txt file (first column: gene name; second column: read count).
Supplementary files format and content: Raw read depth for the phage genome is provided in a .txt file (first column: 1-based genomic position; second column: read depth).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli

growth_protocol: Bacterial cells were grown at 30°C in LB medium supplemented with 10 mM MgSO₄, 0.2% maltose, and 10 μM IPTG, with shaking at 220 rpm. When cultures reached OD₆₀₀ ≈ 0.4, cells were harvested by centrifugation and concentrated to 100× the original density. Infection was initiated by mixing the concentrated host cells with phage lysate (MOI ≈ 4 or ≈ 0.3) or with SM buffer for mock infection. The infection mixture was incubated on ice for 30 minutes, followed by a 5-minute incubation in a 35°C water bath. The culture was then diluted 1:1000 into fresh medium and incubated at 30°C with shaking. Samples were collected at 0+, 2.5, 5, 10, 20, 45, and 60 minutes post-infection.

extract_protocol:
Cell lysis was performed by resuspending the cell pellets in TE buffer containing 1 mg/mL lysozyme and incubating for 5 minutes at room temperature. Subsequent steps—including removal of cell debris, ethanol precipitation of RNA, DNase I treatment, washing, and RNA elution—were carried out using the Quick-RNA Fungal/Bacterial Microprep Kit (Zymo Research) according to the manufacturer's protocol.
The total RNAs were converted into individually barcoded RNA-seq libraries without rRNA depletion with the RNA Library Prep kit from Watchmaker Genomics. Sequencing was performed on a single 10B lane of a NovaSeq X Plus, generating 100-nt single-end reads.

treatment_protocol: Cell cultures were collected and resuspended in 2× volume of RNAprotect Bacteria Reagent (Qiagen), vortexed briefly to mix, and incubated at room temperature for at least 5 minutes. Cells were then pelleted by centrifugation, and the supernatant was discarded.

tag: strain

value: E. coli

value: carrying plasmid pALA3047 (Plac-cfp-ParB)


title: Day 28,Female,Replicate 1

description: Library name: D28_F1


title: Day 7,Female,Replicate 3

description: Library name: D7_F3


title: Day 7,Male,Replicate 1

description: Library name: D7_M1


title: Day 7,Female,Replicate 2

description: Library name: D7_F2


title: Day 4,Male,Replicate 3

description: Library name: D4_M3

value: MI Day 4


title: Day 7,Female,Replicate 1

description: Library name: D7_F1


title: JediLGFP

description: Library name: JediLGFP


title: Day 4,Male,Replicate 2

description: Library name: D4_M2


title: Day 4,Female,Replicate 2

description: Library name: D4_F2


title: JediRGFP

description: Library name: JediRGFP


title: Day 4,Male,Replicate 1

description: Library name: D4_M1


title: Day 1,Male,Replicate 3

description: Library name: D1_M3

value: MI Day 1


title: Day 1,Male,Replicate 2

description: Library name: D1_M2


title: Day 4,Female,Replicate 3

description: Library name: D4_F3


title: Day 4,Female,Replicate 1

description: Library name: D4_F1


title: Day 1,Male,Replicate 1

description: Library name: D1_M1


title: Day 0,Male,Replicate 2

description: Library name: D0_M2

value: Baseline


title: Day 0,Male,Replicate 3

description: Library name: D0_M3


title: Day 1,Female,Replicate 2

description: Library name: D1_F2


title: Day 1,Female,Replicate 1

description: Library name: D1_F1


title: Day 0,Female,Replicate 2

description: Library name: D0_F2


title: Day 0,Male,Replicate 1

description: Library name: D0_M1


title: Day 1,Female,Replicate 3

description: Library name: D1_F3


title: Day 0,Female,Replicate 3

description: Library name: D0_F3


title: Hnrnpu-cKO rep3

first: Yachun

last: An

address: 44 Wenhua West Road, Lixia District, Jinan City

institute: Shandong university

description:
Library name: SAMPLE 6
ko3

data_processing:
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters
The gene expression was estimated by counting number of reads mapped to the genes with featureCounts of subread software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

extract_protocol:
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol.
The cDNA library was sequenced on an Illumina Novaseq6000.

value: liver

value: Hnrnpu-cKO


title: wt rep2

description:
Library name: SAMPLE 2
wt4

value: WT


title: wt rep1

description:
Library name: SAMPLE 1
wt2


title: Hnrnpu-cKO rep1

description:
Library name: SAMPLE 4
ko1


title: Hnrnpu-cKO rep2

description:
Library name: SAMPLE 5
ko2


title: Day 0,Female,Replicate 1

description: Library name: D0_F1


title: wt rep3

description:
Library name: SAMPLE 3
wt11


title: WT / 9262-SB-2

city: Nashville

first: Sujoy

last: Bhattacharya

state: Tennessee

address: 1161 21st Avenue S

department: Ophthalmology and Visual Sciences

institute: Vanderbilt University Medical Center/ Vanderbilt Eye Institute

description: Library name: 9262-SB-2

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023).
An alignment reference was generated from the mm39 mouse genome and GENCODE comprehensive gene annotations (vM31), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter.
About 174-216 million reads were acquired per sample. DESeq2 package v1.42.0 (Love et al. 2014) was used to perform sample-level quality control, low count filtering, normalization and downstream differential gene expression analysis.
Assembly: mm39
Supplementary files format and content: csv file containing raw counts for each sample
Supplementary files format and content: csv file containing normalized counts for each sample

source_name: mouse retinal pigment epithelium (RPE)

growth_protocol: The mouse RPE cells were cultured in culturing medium containing N1 medium supplement (1/100 vol/vol), glutamine (1/100 vol/vol), penicillin-streptomycin (1/100 vol/vol), non-essential amino acid (1/100 vol/vol), hydrocortisone (20μg/mL), taurine (250 mg/L), triiodo-thyronin (0.013μg/L), 5% FBS in alpha-MEM at 37°C in 5% CO2 and media replaced three times a week.

extract_protocol:
RNA isolation from WT and Prom1-KO mRPE cells were performed using Trizol (Invitrogen) and RNeasy (Qiagen), followed by RNA QC per sample
RNA libraries were prepared using Stranded mRNA (NEB) Library prep kit following manufacturer's protocol

treatment_protocol: We used the Cre-loxP approach to delete the Prom1 gene from the mouse RPE in situ.  To knock out Prom1 from mRPE cells in vitro, we used CRISPR/Cas9-mediated gene editing. mRPE cells were cultured in 6-well plates. The cells were allowed to reach 70% confluency and transduced with 10ml lentiviral Cas9 construct with 2ml polybrene. After 24h, the infected cells were subcultured in media containing 1.5mg/ml puromycin and grown until 90% confluency. The cells were selected in media containing 0.5mg/ml puromycin for another week. After puromycin selection, the stably expressing Cas9-mRPE cells were transfected with Prom1 (chromosome 5) synthetic guide RNA (gRNA) sequence (5’-CGTTGCTGCAACAAATGCGG-3’) (ThermoFisher Scientific, catalog # A35533) using Lipofectamine CRISPRMAX transfection reagent (ThermoFisher, Cat # CMAX00008) to target the mouse Prom1 gene at exon 5, following the manufacturer’s protocol. Prom1-KO was verified by genomic DNA analysis. Cas9-expressing mRPE cells were transfected with scrambled or Prom1 gRNA, and these cells were used to extract the genomic DNA using the QIAamp DNA micro kit. PCR was performed using the forward primer: 5’- GTGCATACTGGGGTCCTCAC-3’ and reverse primer: Reverse: 5’-ATCTCCCTGCAACACCCTAA-3’ and Qiagen Taq PCR master mix kit. Genomic sequences were BLAST analyzed to confirm the WT and different Prom1-KO sequences.

value: mouse retinal pigment epithelium (RPE)

value: mRPE WT


title: WT / 9262-SB-1

description: Library name: 9262-SB-1


title: Prom1_KO / 9262-SB-4

description: Library name: 9262-SB-4

value: mRPE Prom1KO 22


title: Prom1_KO / 8995-SB-2

description: Library name: 8995-SB-2


title: WT / 9262-SB-3

description: Library name: 9262-SB-3


title: Prom1_KO / 8995-SB-3

description: Library name: 8995-SB-3

value: mRPE Prom1KO 26


title: WT / 8995-SB-1

description: Library name: 8995-SB-1


title: Prom1_KO / 12965-SB-05

description: Library name: 12965-SB-05


title: Prom1_KO / 12965-SB-04

description: Library name: 12965-SB-04


title: Prom1_KO / 12965-SB-06

description: Library name: 12965-SB-06


title: WT / 12965-SB-02

description: Library name: 12965-SB-02


title: WT / 12965-SB-01

description: Library name: 12965-SB-01


title: KO splenic DCs control 3

city: Philadelphia

first: Adriana

last: Mantegazza

address: 233 South 10th Street

department: Microbiology and Immunology

institute: Thomas Jefferson University

description: Library name: Sample 12

data_processing:
Original image data files were transformed to sequence reads (raw data) using Illumina Casava version 1.8. Raw reads were then filtered to remove adapter contamination, uncertain nucleotides when they constitute more than 10 per cent of either read (N > 10%) and low quality nucleotides (base quality < 5) by Novogene.
HISAT2 software was used for read alignment to the reference genome.
Assembly: mouse genome mm10
Supplementary files format and content: Gene expression quantification (gene counts; xlsm)

source_name: spleen

growth_protocol: Splenic DCs were isolated from WT and SLC29A3-/- mice, from single-cell suspensions of splenocytes by negative selection of B, T, and NK cells with a cocktail of biotin-conjugated antibodies (to CD90.2, CD45R, and CD49b) and anti-biotin microbeads (Miltenyi Biotec Inc., Auburn, CA), followed by positive selection with anti-CD11c (N418) microbeads (Miltenyi Biotec), and magnetic isolation on MACS columns (Miltenyi Biotec). Splenic DCs were phenotyped by flow cytometry and confirmed to be a mixed population of cDC1 (CD11c+ CD8+) and cDC2 (CD11c+ SIRPα+).

extract_protocol:
Total RNA was isolated from splenic DCs using the RNeasy Micro kit (Qiagen, Germantown, MD).
Library construction was performed at Novogene Corporation using random hexamer primers. RNA sequencing was performed using Illumina NovaSeq 6000 PE150 sequencing platform.

treatment_protocol: Splenic DCs were untreated or treated with attenuated Salmonella typhimurium (STmDfla) at MOI:10 for 3 hours.

value: spleen

value: splenic DCs

value: untreated


title: Prom1_KO / 9262-SB-6

description: Library name: 9262-SB-6


title: KO splenic DCs control 2

description: Library name: Sample 10


title: WT splenic DCs control 3

description: Library name: Sample 6

value: WT C57BL6


title: KO splenic DCs treated 2

description: Library name: Sample 9

value: STmDfla


title: WT splenic DCs treated 3

description: Library name: Sample 5


title: WT splenic DCs control 2

description: Library name: Sample 4


title: WT splenic DCs control 1

description: Library name: Sample 2


title: Prom1_KO / 9262-SB-5

description: Library name: 9262-SB-5


title: WT splenic DCs treated 2

description: Library name: Sample 3


title: M391_Resp_T2_FNA_72R

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

description: Library name: M391_Resp_T2_FNA_72R

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v2.10)
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.11.9)
Reads were aligned to the Gencode GRCm38.p6 genome using STAR (v2.7.8a). Gencode vM24 gene annotations were provided to STAR to improve the accuracy of mapping.
featureCounts (v2.0.2) was used to count the number of mapped reads to each gene
Assembly: GRCm38.p6
Supplementary files format and content: Count files includes the raw counts for each sample

source_name: EMT6 tumor

growth_protocol: EMT6 cells were cultured in DMEM/F12 with 10% FBS prior to injection into BALB/c mice

extract_protocol:
RNA was harvested using the Maxwell 16 automated workstation (Promega) using the LEV simplyRNA Tissue or Blood purification kit (Promega).
NEBNext rRNA Depletion Kit

treatment_protocol: 5x104 EMT6 cells were injected into 4th mammary fat pad of BALB/c mice, mIgG1 or anti-PD-L1 were administered at an initial dose of 200 ug intraperitoneally when individual mouse tumors reached 100 mm3 and subsequently dropped to 100ug weekly for up to 4-weeks

tag: time

value: Day 14= 7 days post treatment

tag: response to_anti-pd-l1

value: Responder

value: EMT6 tumor

value: wildtype


title: WT splenic DCs treated 1

description: Library name: Sample 1


title: M401_Resp_T2_FNA_72

description: Library name: M401_Resp_T2_FNA_72


title: M393_Resp_T2_FNA_71

description: Library name: M393_Resp_T2_FNA_71


title: WT / 12965-SB-03

description: Library name: 12965-SB-03


title: M389_Resp_T2_FNA_70

description: Library name: M389_Resp_T2_FNA_70


title: M386_AR_T1_PBMC_7

description: Library name: M386_AR_T1_PBMC_7

source_name: PBMC

value: Day 1= one day before EMT6 injection

value: Acquired resistant

value: PBMC


title: M399_AR_T2_FNA_69

description: Library name: M399_AR_T2_FNA_69


title: M398_IR_T2_FNA_66

description: Library name: M398_IR_T2_FNA_66

value: Intrinsic-resistant


title: M387_IR_T2_FNA_64

description: Library name: M387_IR_T2_FNA_64


title: KO splenic DCs treated 3

description: Library name: Sample 11


title: KO splenic DCs control 1

description: Library name: Sample 8


title: KO splenic DCs treated 1

description: Library name: Sample 7


title: M406_Ctrl_T2_FNA_63

description: Library name: M406_Ctrl_T2_FNA_63


title: M402_Ctrl_T2_FNA_63R

description: Library name: M402_Ctrl_T2_FNA_63R


title: M405_Ctrl_T2_FNA_62

description: Library name: M405_Ctrl_T2_FNA_62


title: M404_Ctrl_T2_FNA_61

description: Library name: M404_Ctrl_T2_FNA_61


title: M393_Resp_T1_FNA_59

description: Library name: M393_Resp_T1_FNA_59

value: Day 7= tumor-bearing, immediately before anti-PD-L1 treatment


title: M391_Resp_T1_FNA_60R

description: Library name: M391_Resp_T1_FNA_60R


title: M398_IR_T1_PBMC_6

description: Library name: M398_IR_T1_PBMC_6


title: M392_AR_T1_PBMC_8

description: Library name: M392_AR_T1_PBMC_8


title: M389_Resp_T1_FNA_58

description: Library name: M389_Resp_T1_FNA_58


title: M386_AR_T1_FNA_55

description: Library name: M386_AR_T1_FNA_55


title: M392_AR_T1_FNA_56

description: Library name: M392_AR_T1_FNA_56


title: M401_Resp_T1_FNA_60

description: Library name: M401_Resp_T1_FNA_60


title: M398_IR_T1_FNA_54

description: Library name: M398_IR_T1_FNA_54


title: M392_AR_T2_FNA_68

description: Library name: M392_AR_T2_FNA_68


title: M402_Ctrl_T1_FNA_51R

description: Library name: M402_Ctrl_T1_FNA_51R

value: Day 7= tumor-bearing, immediately before mIgG1 treatment


title: M405_Ctrl_T1_FNA_50

description: Library name: M405_Ctrl_T1_FNA_50


title: M397_IR_T1_PBMC_5

description: Library name: M397_IR_T1_PBMC_5


title: M387_IR_T1_FNA_52

description: Library name: M387_IR_T1_FNA_52


title: M386_AR_T2_FNA_67

description: Library name: M386_AR_T2_FNA_67


title: M406_Ctrl_T1_FNA_51

description: Library name: M406_Ctrl_T1_FNA_51


title: M397_IR_T1_FNA_53

description: Library name: M397_IR_T1_FNA_53


title: M397_IR_T2_FNA_65

description: Library name: M397_IR_T2_FNA_65


title: M404_Ctrl_T1_FNA_49

description: Library name: M404_Ctrl_T1_FNA_49


title: M401_Resp_T4_PBMC_48

description: Library name: M401_Resp_T4_PBMC_48

value: Day 21= 14 days post treatment


title: M393_Resp_T4_PBMC_47

description: Library name: M393_Resp_T4_PBMC_47


title: M399_AR_T4_PBMC_45

description: Library name: M399_AR_T4_PBMC_45


title: M392_AR_T4_PBMC_44

description: Library name: M392_AR_T4_PBMC_44


title: M389_Resp_T4_PBMC_46

description: Library name: M389_Resp_T4_PBMC_46


title: M386_AR_T4_PBMC_43

description: Library name: M386_AR_T4_PBMC_43


title: M399_AR_T1_FNA_57

description: Library name: M399_AR_T1_FNA_57


title: M398_IR_T4_PBMC_42

description: Library name: M398_IR_T4_PBMC_42


title: M387_IR_T4_PBMC_40

description: Library name: M387_IR_T4_PBMC_40


title: M406_Ctrl_T4_PBMC_39

description: Library name: M406_Ctrl_T4_PBMC_39


title: M397_IR_T4_PBMC_41

description: Library name: M397_IR_T4_PBMC_41


title: M387_IR_T1_PBMC_4

description: Library name: M387_IR_T1_PBMC_4


title: M405_Ctrl_T4_PBMC_38

description: Library name: M405_Ctrl_T4_PBMC_38


title: M391_Resp_T3_PBMC_36R

description: Library name: M391_Resp_T3_PBMC_36R


title: M393_Resp_T3_PBMC_35

description: Library name: M393_Resp_T3_PBMC_35


title: M404_Ctrl_T4_PBMC_37

description: Library name: M404_Ctrl_T4_PBMC_37


title: M401_Resp_T3_PBMC_36

description: Library name: M401_Resp_T3_PBMC_36


title: M402_Ctrl_T4_PBMC_39R

description: Library name: M402_Ctrl_T4_PBMC_39R


title: M392_AR_T3_PBMC_32

description: Library name: M392_AR_T3_PBMC_32


title: M389_Resp_T3_PBMC_34

description: Library name: M389_Resp_T3_PBMC_34


title: M386_AR_T3_PBMC_31

description: Library name: M386_AR_T3_PBMC_31


title: M399_AR_T3_PBMC_33

description: Library name: M399_AR_T3_PBMC_33


title: M397_IR_T3_PBMC_29

description: Library name: M397_IR_T3_PBMC_29


title: M398_IR_T3_PBMC_30

description: Library name: M398_IR_T3_PBMC_30


title: M406_Ctrl_T1_PBMC_3

description: Library name: M406_Ctrl_T1_PBMC_3


title: M391_Resp_T4_PBMC_48R

description: Library name: M391_Resp_T4_PBMC_48R


title: M402_Ctrl_T3_PBMC_27R

description: Library name: M402_Ctrl_T3_PBMC_27R


title: M406_Ctrl_T3_PBMC_27

description: Library name: M406_Ctrl_T3_PBMC_27


title: M391_Resp_T2_PBMC_24R

description: Library name: M391_Resp_T2_PBMC_24R


title: M404_Ctrl_T3_PBMC_25

description: Library name: M404_Ctrl_T3_PBMC_25


title: M405_Ctrl_T3_PBMC_26

description: Library name: M405_Ctrl_T3_PBMC_26


title: M401_Resp_T2_PBMC_24

description: Library name: M401_Resp_T2_PBMC_24


title: M393_Resp_T2_PBMC_23

description: Library name: M393_Resp_T2_PBMC_23


title: M399_AR_T2_PBMC_21

description: Library name: M399_AR_T2_PBMC_21


title: M392_AR_T2_PBMC_20

description: Library name: M392_AR_T2_PBMC_20


title: M405_Ctrl_T1_PBMC_2

description: Library name: M405_Ctrl_T1_PBMC_2


title: M387_IR_T2_PBMC_16

description: Library name: M387_IR_T2_PBMC_16


title: M398_IR_T2_PBMC_18

description: Library name: M398_IR_T2_PBMC_18


title: M397_IR_T2_PBMC_17

description: Library name: M397_IR_T2_PBMC_17


title: M402_Ctrl_T2_PBMC_15R

description: Library name: M402_Ctrl_T2_PBMC_15R


title: M406_Ctrl_T2_PBMC_15

description: Library name: M406_Ctrl_T2_PBMC_15


title: M405_Ctrl_T2_PBMC_14

description: Library name: M405_Ctrl_T2_PBMC_14


title: M404_Ctrl_T2_PBMC_13

description: Library name: M404_Ctrl_T2_PBMC_13


title: M387_IR_T3_PBMC_28

description: Library name: M387_IR_T3_PBMC_28


title: M401_Resp_T1_PBMC_12

description: Library name: M401_Resp_T1_PBMC_12


title: M393_Resp_T1_PBMC_11

description: Library name: M393_Resp_T1_PBMC_11


title: M389_Resp_T1_PBMC_10

description: Library name: M389_Resp_T1_PBMC_10


title: M402_Ctrl_T1_PBMC_03R

description: Library name: M402_Ctrl_T1_PBMC_03R


title: M404_Ctrl_T1_PBMC_1

description: Library name: M404_Ctrl_T1_PBMC_1


title: M17973_Resp_T6_P6

description: Library name: M17973_Resp_T6_P6

value: Day 35= 28 days post treatment


title: M17973_Resp_T5_P6

description: Library name: M17973_Resp_T5_P6

value: Day 28= 21 days post treatment


title: M17973_Resp_T3_P6

description: Library name: M17973_Resp_T3_P6


title: M17973_Resp_T4_P6

description: Library name: M17973_Resp_T4_P6


title: M17970_AR_T4_P6

description: Library name: M17970_AR_T4_P6


title: M17970_AR_T5_P6

description: Library name: M17970_AR_T5_P6


title: M17973_Resp_T1_P6

description: Library name: M17973_Resp_T1_P6


title: M17970_AR_T3_P6

description: Library name: M17970_AR_T3_P6


title: M17973_Resp_T2_P6

description: Library name: M17973_Resp_T2_P6


title: M386_AR_T2_PBMC_19

description: Library name: M386_AR_T2_PBMC_19


title: M17970_AR_T2_P6

description: Library name: M17970_AR_T2_P6


title: M17970_AR_T1_P6

description: Library name: M17970_AR_T1_P6


title: M389_Resp_T2_PBMC_22

description: Library name: M389_Resp_T2_PBMC_22


title: M17969_IR_T4_P6

description: Library name: M17969_IR_T4_P6


title: M17969_IR_T3_P6

description: Library name: M17969_IR_T3_P6


title: M17969_IR_T1_P6

description: Library name: M17969_IR_T1_P6


title: M17969_IR_T5_P6

description: Library name: M17969_IR_T5_P6


title: M17968_Ctrl_T2_P6

description: Library name: M17968_Ctrl_T2_P6


title: M17968_Ctrl_T3_P6

description: Library name: M17968_Ctrl_T3_P6


title: M17969_IR_T2_P6

description: Library name: M17969_IR_T2_P6


title: M17964_IR_T5_P6

description: Library name: M17964_IR_T5_P6


title: M17964_IR_T4_P6

description: Library name: M17964_IR_T4_P6


title: M17964_IR_T2_P6

description: Library name: M17964_IR_T2_P6


title: M17964_IR_T1_P6

description: Library name: M17964_IR_T1_P6


title: M17962_Resp_T6_P6

description: Library name: M17962_Resp_T6_P6


title: M17962_Resp_T5_P6

description: Library name: M17962_Resp_T5_P6


title: M17962_Resp_T4_P6

description: Library name: M17962_Resp_T4_P6


title: M17962_Resp_T3_P6

description: Library name: M17962_Resp_T3_P6


title: M17962_Resp_T2_P6

description: Library name: M17962_Resp_T2_P6


title: M17962_Resp_T1_P6

description: Library name: M17962_Resp_T1_P6


title: M17961_AR_T5_P6

description: Library name: M17961_AR_T5_P6


title: M17961_AR_T4_P6

description: Library name: M17961_AR_T4_P6


title: M17958_Ctrl_T4_P6

description: Library name: M17958_Ctrl_T4_P6


title: M17958_Ctrl_T3_P6

description: Library name: M17958_Ctrl_T3_P6


title: M17961_AR_T1_P6

description: Library name: M17961_AR_T1_P6


title: M17958_Ctrl_T2_P6

description: Library name: M17958_Ctrl_T2_P6


title: M17961_AR_T3_P6

description: Library name: M17961_AR_T3_P6


title: M17968_Ctrl_T4_P6

description: Library name: M17968_Ctrl_T4_P6


title: M17958_Ctrl_T1_P6

description: Library name: M17958_Ctrl_T1_P6


title: M17956_IR_T3_P6

description: Library name: M17956_IR_T3_P6


title: M17956_IR_T2_P6

description: Library name: M17956_IR_T2_P6


title: M17968_Ctrl_T1_P6

description: Library name: M17968_Ctrl_T1_P6


title: M17956_IR_T1_P6

description: Library name: M17956_IR_T1_P6


title: M17964_IR_T3_P6

description: Library name: M17964_IR_T3_P6


title: M17955_AR_T5_P6

description: Library name: M17955_AR_T5_P6


title: M17955_AR_T3_P6

description: Library name: M17955_AR_T3_P6


title: M17955_AR_T4_P6

description: Library name: M17955_AR_T4_P6


title: M17955_AR_T2_P6

description: Library name: M17955_AR_T2_P6


title: M17955_AR_T1_P6

description: Library name: M17955_AR_T1_P6


title: M17953_Ctrl_T4_P6

description: Library name: M17953_Ctrl_T4_P6


title: M17953_Ctrl_T3_P6

description: Library name: M17953_Ctrl_T3_P6


title: M17953_Ctrl_T2_P6

description: Library name: M17953_Ctrl_T2_P6


title: M17961_AR_T2_P6

description: Library name: M17961_AR_T2_P6


title: M17951_Resp_T5_P6

description: Library name: M17951_Resp_T5_P6


title: M17951_Resp_T6_P6

description: Library name: M17951_Resp_T6_P6


title: M17951_Resp_T4_P6

description: Library name: M17951_Resp_T4_P6


title: M17951_Resp_T3_P6

description: Library name: M17951_Resp_T3_P6


title: M17951_Resp_T2_P6

description: Library name: M17951_Resp_T2_P6


title: M17956_IR_T4_P6

description: Library name: M17956_IR_T4_P6


title: M17951_Resp_T1_P6

description: Library name: M17951_Resp_T1_P6


title: Lhx1os pull-down LacZ Replicate1

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description: Library name: lhx1os_lacz1_S36

data_processing:
Reads were processed using Cutadapt v3.2 with -u 1 -U 1 –trim-n –nextseq-trim=20 -m 35 parameters to trim low-quality bases and sequencing artifacts
Reads aligning to the sequence of murine rRNAs (retrieved from NCBI Gene database77), 7SL or 7SK transcripts (retrieved from Ensembl database) were filtered out; this first alignment was conducted using Bowtie2 v2.4.2, aligning the first read in each pair with the --nofw parameter and the second read with the --norc parameter. Only read pairs in which both mates did not map were retained for downstream analysis.
PCR duplicates were removed from all samples using MarkDuplicates command from Picard suite.
Uniquely mapping fragments were counted for each annotated gene (Ensembl release 99) using Htseq (v0.13.5).
Assembly: GRCm38
Supplementary files format and content: counts_table.txt is a tab/comma-delimited file containing the raw counts for each annotated gene in each sample
Supplementary files format and content: FPKM_table.txt is a tab/comma-delimited file containing the FPKM values for each annotate gene in each sample

source_name: mESC derived motor neurons

growth_protocol: Murine HBG3 ES cells were cultured on gelatin-coated or MEF-coated dishes and maintained in mESC medium (Dulbecco’s Modified Eagle’s Medium for ES, 15% Fetal Bovine Serum for ES, 1X GlutaMAX, 1X Non Essential AmminoAcids, 1X nucleosides, 1X 2-mercaptoethanol and 1X Penicillin/Streptomycin) supplemented with LIF (103 unit/mL), FGFRi (1,5 μM) and Gsk-3i (1,5 μM) (LIF+2i condition). Medium was changed every day and cells were passaged every 2–3 days with 1X Trypsin-EDTA solution. Cells were grown at 37°C, 5% CO2.

extract_protocol:
Total RNA was isolated from cell cultures using miRNeasy Kit (Qiagen) according to the manufacturer’s protocol.
Library preparation was performed using Stranded Total RNA Prep with Ribo- Zero Plus (Illumina) according to manufacturer's documentation.

treatment_protocol: Spinal motor neurons (MNs) were differentiated from mESCs HB9::GFP according to Wichterle et al. (doi:10.1002/9780470151808.sc01h01s5.) and Errichelli et al (https://doi.org/10.1038/ncomms14741).  After papain dissociation, cells were plated on polyornithine/laminin-coated dishes with N2B27 medium (50% DMDM F12, 50% Neurobasal, 1X Glutamax, 1X Penicillin-Streptomycin, 1X B27, 1X N2, 200 ng/mL Ascorbic Acid, 20 ng/mL BDNF, 10 ng/mL CNTF, 10 ng/mL GDNF, 10 nM Rhok inhibitor) and differentiation was allowed to proceed for three additional days.

value: mESC derived motor neurons

value: Control pull-down sample obtained using LacZ probe set

tag: batch


title: Lhx1os pull-down ODD Replicate2

description: Library name: lhx1os_odd2_S38

value: Lhx1os pull-down sample obtained using ODD probe set


title: M17953_Ctrl_T1_P6

description: Library name: M17953_Ctrl_T1_P6


title: Lhx1os pull-down LacZ Replicate2

description: Library name: lhx1os_lacz2_S40


title: Lhx1os pull-down ODD Replicate1

description: Library name: lhx1os_odd1_S34


title: Lhx1os pull-down EVEN Replicate2

description: Library name: lhx1os_even2_S39

value: Lhx1os pull-down sample obtained using EVEN probe set


title: Lhx1os pull-down Input Replicate2

description: Library name: lhx1os_input2_S37

value: Input sample from mESC-derived motor neurons


title: M17956_IR_T5_P6

description: Library name: M17956_IR_T5_P6


title: Lhx1os pull-down Input Replicate1

description: Library name: lhx1os_input1_S33


title: Lhx1os pull-down EVEN Replicate1

description: Library name: lhx1os_even1_S35


title: Treat2

city: Guangzhou

first: Yanteng

last: Xu

state: Guangdong

address: 600# Tianhe Road

department: Centre for Nanomedicine

institute: The Third Affiliated Hospital of Sun Yat-sen University

description:
Library name: Treat2
T2

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (https://ftp.ensembl.org/pub/release-113/fasta/mus_musculus_c57bl6nj/dna/) to map reads to the reference genome of mus musculus Ensembl_v113. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: mus_musculus Ensembl_v113
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: Striatum

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

value: Striatum

tag: group

value: treated


title: Normal1

description:
Library name: Normal1
N1

value: normal


title: HD2

description:
Library name: HD2
H2

value: HD


title: HD1

description:
Library name: HD1
H1


title: Normal2

description:
Library name: Normal2
N2