title: Library9b RNA-seq rep2

city: Saint Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 660 South Euclid Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

description: RNA-seq performed on reporter gene barcode amplicons

data_processing:
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified using custom python scripts.
Demultiplexed reads were used to determine the read counts for each barcode with custom python scripts.
To obtain barcode read counts, reads were matched to barcoded reporter gene sequences using custom python scripts. Only exact barcoded matches were counted. FASTA files with reporter gene sequences for each library are included as supplementary files.
Assembly: mm10
Supplementary files format and content: Each sample has its own tab-delimited file. Column 1: Barcode sequence. Column 2: cis-regulatory element name. Column 3: Barcode counts.

source_name: whole retina

growth_protocol: P0 mouse retinal explants were electroporated with plasmid library and cultured ex vivo for 8 days.

extract_protocol:
RNA was extracted from retinas with TRIzol and treated with Turbo Dnase. cDNA was prepared using SuperScript IV.
Sequence barcodes from reporter genes were amplified by PCR and purified with Monarch PCR cleanup kit. Custom Illumina adapters were added by PCR.

value: whole retina

value: wild-type


title: Library9b RNA-seq rep1

status: Public on Sep 01 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: HeLa cells,LbNOX, 24h dox 1

city: San Diego

first: Xingxiu

last: Pan

state: California

address: 6868 Nancy Ridge Dr

institute: Scintillon institute

data_processing:
Illumina HiSeq X reads were trimmed and clipped for quality control inTrimmomatic v.0.36.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality。
Using the STAR aligner v.2.5.2b., the trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Counts were then processed in R using the DESeq2 package
Assembly: GRCh38
Supplementary files format and content: unique hit counts for each sample:sample.counts.txt
Supplementary files format and content: hit count for all the gene

organism: Homo sapiens

source_name: Uterus; Cervix

growth_protocol: Hela cells were cultured in DMEM+FBS [Dulbecco's Modified Eagle Medium without pyruvate and glucose supplemented with 25 mM glucose, 10% non-dialyzed FBS and 1% penicillin/streptomycin  at 37C in an atmosphere of 5% CO2

extract_protocol:
Twenty-four hours after addition of doxycycline, cells were harvested, and cell pellets were snapfrozen.Samples were submitted to GENEWIZ for NGS RNA sequencing.
RNA libraries for RNA-seq were prepared using polyA selection.

treatment_protocol: Twenty-four hours later, media was exchanged with 10 mL of DMEM+dFBS ± 300 ng/mL Dox.

value: Uterus; Cervix

tag: cell line

value: HeLa

tag: cell type

value: epithelial cell

value: LbNOX

value: 24h doxycycline


title: Library9a RNA-seq rep1


title: HeLa cells,Luciferase, 24h dox 1

value: Luciferase


title: CD45+ cells, Apoe/Cd36 double-null HFD, scRNA-seq

city: Wauwatosa

first: Yiliang

last: Chen

address: 8727 W Watertown Plank

institute: Versiti

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Assembly: mm10
Supplementary files format and content: Tab-seperated files and matrix files

source_name: adipose tissue

extract_protocol:
Mice were sacrificed and perfused with 10 ml PBS to remove peripheral blood from the adipose tissues. Then epididymal visceral white adipose tissue (eWAT) was isolated and washed with ice-cold PBS. eWAT was minced into 2-3 mm pieces by scissors and transferred to gentleMACS C-tubes (Miltenyi Biotec) with 1.5 ml enzymatic digestion mixture (Liberase, 0.77 mg/ml; Hyaluronidase, 0.3 mg/ml; Deoxyribonuclease, 0.3 mg/ml; BSA, 1mg/ml; CaCl2, in PBS). Tissues were digested in a gentle MACSTM Octo Dissociator with Heaters (Miltenyi Biotec) at 37°C for 30 min. Suspensions were immediately filtered with a 70 mm cell strainer (Fisher Scientific) and washed once with FACS buffer (5% FBS and 0.1% sodium azide in PBS). Then, CD45+ cells were selected by the EasySep Mouse CD45 Positive Selection Kit (STEMCELL Technologies). The CD45+ cells were then suspended in the FACS buffer, counted, and immediately loaded onto a 10X Genomics Chromium instrument according to the instructions from the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, Pleasanton, CA, USA). 5,000 live cells per condition were loaded onto each GEM.
library construction was perfrmed according to the instruction from the Chromium Next GEM Single Cell 3' Reagent Kits v3.1

value: adipose tissue

value: Apoe/Cd36 double-null

value: HFD 10 weeks


title: Library7 RNA-seq rep2


title: Library7 RNA-seq rep3


title: CD45+ cells, Apoe-null HFD, scRNA-seq

value: Apoe-null


title: Library6 RNA-seq rep2


title: Library4 RNA-seq rep3


title: Library5 RNA-seq rep2


title: Library7 RNA-seq rep1


title: Library9b RNA-seq rep3


title: Library4 RNA-seq rep2


title: Library9a RNA-seq rep3


title: Library5 RNA-seq rep3


title: Library5 RNA-seq rep1


title: Library6 RNA-seq rep3


title: Library9a RNA-seq rep2


title: HeLa cells,mitoEcSTH, 24h dox 1

value: mitoEcSTH


title: Library3 RNA-seq rep4


title: Library3 RNA-seq rep6


title: Library6 RNA-seq rep1


title: Single granulosa cell (LCM) GC095_S61

city: Kashihara

first: Hiroki

last: Ikeda

address: 840 Shijo-Cho, Kashihara, Nara

country: Japan

institute: Nara Medical University

description: DRaqL - SC3-seq

data_processing:
After trimming polyA/T sequences, adapter sequences, and poor quality reads, using fastp (v. 0.20.0) and cutadapt (ver. 1.16), the sequenced reads were aligned to the GRCm38 mouse genome assemblywith ERCC spike-in RNA sequences using the HiSAT2 (v. 2.1.0).
Best-matched reads on annotated genes were counted using HTSeq 0.10.0 with a modified GRCm38 gtf file which is extended up to 10 Kb downstream from transcription termination sites of reference genes.
Mapped reads on exons and exon-exon junctions were counted by featureCounts (v2.0.1) with the GRCm38 gtf file and the option "-J" "-p" "-M" "-O" "-t　exon" "-g　transcript_id".
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw read counts.

molecule: polyA RNA

source_name: Ovary

extract_protocol:
Cells were isolated with LCM in 6.4 μL of cell lysis buffer (0.6 μL of 5× SuperScript II buffer, 0.1 μL of 100 μM Oligo dT VN, 0.8 μL of dNTP mix [25 mM each], 0.25 μL of 40 U/μL recombinant RNase inhibitor [Takara Bio], 0.5 μL of 100 mM DTT, 0.06 μL of 1 M MgCl2 [Sigma-Aldrich], 2 μL of 5 M Betaine [Sigma-Aldrich], 0.16 μL of 1:500,000 diluted ERCC RNA Spike-In Mix 1, 0.4 μL of 5% SDc, and 1.53 μL of DDW) in the caps of PCR tubes, and spun down into the tubes by brief centrifugation. The isolated cells were lysed at 72°C for 6 min, followed by addition of 2.8 μL quenching buffer (0.7 μL of Triton X-100, 0.7 μL of 2% BSA, and 1.4 μL of 5× SuperScript II buffer [Thermo Fisher]).
1.6 μL of a template-switching mixture (0.1 μL of 100 μM N-template-switching oligo, 0.25 μL of SuperScript II, 0.25 μL of SuperScript III, 0.2 μL of recombinant RNase inhibitor, and 0.8 μL of DDW) was added to cell lysate in the lysis buffer of smart-seq2, followed by the cycling RT program for DRaqL-Smart-seq2. Then, cDNA amplification was performed by adding 15 μL of Seq amp PCR mixture (12.5 μL of 2x SeqAmp buffer (Takara Bio), 0.05 μL of 100 μM N-IS PCR primer, 0.5 μL of SeqAmp DNA polymerase (Takara Bio), and 1.95 μL of DDW) and applying the SeqAmp thermal cycling program. For oocytes, we used a PCR program of 18 cycles. The amplified cDNA (25.8 μL) was purified with a 0.8× volume of AxyPrep MAG PCR clean-up reagent according to the manufacturer’s instructions. Libraries of the cDNAs amplified with the Smart-seq2-based methods were prepared using the library construction module of the SMART-Seq v4 3' DE Kit, according to the manufacturer's instructions. Briefly, 10 to 12 purified cDNA samples were pooled and purified with a 0.8× volume of Axyprep reagent. 300 pg to 400 pg cDNAs were tagmented using the Amplicon Tagment Mix (ATM) of the Illumina Nextera XT DNA Sample Preparation Kit (Illumina). 3’-ends of the tagmented cDNAs were amplified with Nextera PCR Master Mix and dual index primers (Reverse PCR primer HT Index and Tn Forward PCR Primer HT Index in the SMART-Seq v4 3' DE Kit) designed for TnRP1 and TnRP2 sequences. All libraries were mixed and sequenced using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles) with paired-end mode using Read2 (8 bps) for the in-line index and with dual-index mode (8 bps).

value: Ovary

tag: collecting condition

value: LCM

value: Granulosa cell

tag: feature

value: Neighboring


title: Single granulosa cell (LCM) GC081_S51

description: DRaqL - SC3-seq

value: Non-neighboring


title: Library4 RNA-seq rep1

value: whole retina

value: wild-type


title: Single oocyte(Raw (fresh), Smart-Seq2) IL12_SS2_RawPair08_S8

value: Raw (fresh)

value: Oocyte

value: Grown


title: Library3 RNA-seq rep5


title: Library3 RNA-seq rep3


title: Single oocyte(Raw (fresh), Smart-Seq2) IL08_SS2_RawPair08_S8


title: Library3 RNA-seq rep1


title: Single granulosa cell (LCM) GC085_S54

description: DRaqL - SC3-seq


title: Single oocyte(Raw (fresh), Smart-Seq2) IL06_SS2_RawPair08_S8


title: Single oocyte(Raw (fresh), Smart-Seq2) IL04_SS2_RawPair06_S6


title: Single oocyte(Raw (fresh), Smart-Seq2) IL11_SS2_RawPair08_S8


title: Single oocyte(Raw (fresh), Smart-Seq2) IL05_SS2_RawPair08_S8


title: Single oocyte(Raw (fresh), Smart-Seq2) IL10_SS2_RawPair08_S8


title: Single oocyte(Raw (fresh), Smart-Seq2) IL10_SS2_RawPair02_S2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL09_SS2_RawPair04_S4


title: Single oocyte(Raw (fresh), Smart-Seq2) IL01_SS2_RawPair01_S1


title: Single oocyte(Raw (fresh), Smart-Seq2) IL07_SS2_RawPair04_S4


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL07_SS2_RawPair01_S1


title: Single oocyte(Raw (fresh), Smart-Seq2) IL09_SS2_RawPair08_S8


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL08_SS2_RawPair03_S3


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL05_SS2_RawPair01_S1


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL02_SS2_RawPair05_S5


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL03_SS2_RawPair05_S5


title: Single oocyte(Raw (fresh), Smart-Seq2) IL03_SS2_RawPair08_S8


title: Single oocyte(Raw (fresh), Smart-Seq2) IL02_SS2_RawPair08_S8


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL12_SS2_RawPair04_S4


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL01_SS2_RawPair05_S5


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL10_SS2_RawPair01_S1


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL10_SS2_RawPair03_S3


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL10_SS2_RawPair04_S4


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL05_SS2_RawPair07_S7


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL06_SS2_RawPair05_S5


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL05_SS2_RawPair02_S2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL11_SS2_RawPair01_S1


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL09_SS2_RawPair01_S1


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL08_SS2_RawPair01_S1


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL04_SS2_RawPair02_S2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL03_SS2_RawPair07_S7


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL03_SS2_RawPair06_S6


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL01_SS2_RawPair02_S2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL06_SS2_RawPair03_S3


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL06_SS2_RawPair06_S6


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL06_SS2_RawPair01_S1


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL11_SS2_RawPair03_S3


title: Single oocyte(LCM, DRaqL - Smart-seq2) IL07_SS2_LCMPair08_S16

description: DRaqL - Smart-seq2

value: Secondary-antral


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL05_SS2_RawPair05_S5


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL04_SS2_RawPair05_S5


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL04_SS2_RawPair01_S1


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL03_SS2_RawPair01_S1


title: Single oocyte(Raw (fresh), Smart-Seq2) IL01_SS2_RawPair08_S8


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL12_SS2_LCMPair01_S9

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL12_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL12_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL09_SS2_RawPair03_S3


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL09_SS2_RawPair05_S5


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL11_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL02_SS2_RawPair01_S1


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL11_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL07_SS2_RawPair05_S5


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL10_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL09_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL09_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL06_SS2_RawPair02_S2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL09_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single oocyte(LCM, DRaqL - Smart-seq2) IL11_SS2_LCMPair08_S16

description: DRaqL - Smart-seq2


title: Single granulosa cell(Raw (fresh), Smart-Seq2) IL02_SS2_RawPair02_S2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL07_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL06_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single oocyte(LCM, DRaqL - Smart-seq2) IL08_SS2_LCMPair08_S16

description: DRaqL - Smart-seq2


title: Single oocyte(LCM, DRaqL - Smart-seq2) IL10_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single oocyte(LCM, DRaqL - Smart-seq2) IL09_SS2_LCMPair08_S16

description: DRaqL - Smart-seq2


title: Single oocyte(LCM, DRaqL - Smart-seq2) IL04_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single oocyte(LCM, DRaqL - Smart-seq2) IL05_SS2_LCMPair08_S16

description: DRaqL - Smart-seq2


title: Single oocyte(LCM, DRaqL - Smart-seq2) IL04_SS2_LCMPair08_S16

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL06_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL11_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL10_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL04_SS2_LCMPair04_S12

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL04_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL08_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL08_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL02_SS2_LCMPair04_S12

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL12_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL01_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL02_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL07_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL07_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL01_SS2_LCMPair04_S12

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL06_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL05_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL06_SS2_LCMPair04_S12

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL12_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL11_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL01_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL12_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL04_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL10_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL03_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL03_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL10_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL02_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL09_SS2_LCMPair01_S9

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL03_SS2_LCMPair02_S10

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL11_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL12_SS2_LCMPair04_S12

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL10_SS2_LCMPair04_S12

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL08_SS2_LCMPair04_S12

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL09_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL09_SS2_LCMPair04_S12

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL07_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL08_SS2_LCMPair01_S9

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL08_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL08_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL06_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL06_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL05_SS2_LCMPair06_S14

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL07_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL05_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL02_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL03_SS2_LCMPair01_S9

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL03_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL05_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL04_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL04_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL02_SS2_LCMPair01_S9

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL03_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL02_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL01_SS2_LCMPair07_S15

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL10_SS2_LCMPair01_S9

description: DRaqL - Smart-seq2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL01_SS2_LCMPair03_S11

description: DRaqL - Smart-seq2


title: Tip49flox/-_4-OHT_2

city: Kyoto

first: Ayuna

last: Hattori

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo

institute: Kyoto University

data_processing:
CLC Genomics Workbench
Raw quantification output is Total Count for each gene (GE files) or transcript (TE files), for each sample
Mapped reads exported, converted into bedgraph for visualization in UCSC browser
PCA plot and box plot of total count (N>1 experiment) or RPKM (N=1 experiment)
Assembly: mm10
Supplementary files format and content: After statistical analysis (explained in next page), CLC files are exported in Excel format. For CLC Main Workbench users, CLC files can be provided in zip archive format.

source_name: leukemia

extract_protocol:
Trizol
Standard: 500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420) • Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420)

value: leukemia

value: Tip49 cKO


title: WT_Tip inhibitor_2

value: WT

value: Tip inhibitor


title: Tip49flox/-_no treatment_2

value: non


title: Tip49flox/-_4-OHT_1


title: WT_Tip inhibitor_1


title: Tip49flox/-_no treatment_1


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL07_SS2_LCMPair01_S9

description: DRaqL - Smart-seq2


title: WT_no tretement_1


title: WT_no tretement_2


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL02_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2


title: CD4+ FOXP3+ Treg, venetoclax, spleen, biol rep 2

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

description: ATAC-seq

library_source: genomic

data_processing:
Reads were trimmed using SeqPurge
Aligned using Bowtie2
Reads were filtered for alignment quality > q30 and purged of duplicates using Picard
Peaks called using MACS2
Assembly: mm10
Supplementary files format and content: 35kSpleenTreatedvsUntreatedChromVARdeviationScore.txt

molecule: genomic DNA

source_name: Spleen

extract_protocol:
Cells lysed and nuclei were transposed using Illumina Tagment buffer and enzyme
Libraries prepared using Nextera Index Kit

treatment_protocol: FOXP3-IRES-GFP mice were treated for 14 days with vehicle or 50mg/kg venetoclax

value: Spleen

tag: strain

value: B6.Cg-Foxp3tm2Tch/J (FOXP3-IRES-GFP)

value: Venetoclax


title: CD4+ FOXP3+ Treg, venetoclax, spleen, biol rep 1

description: ATAC-seq


title: CD4+ FOXP3+ Treg, vehicle, spleen, biol rep 1

description: ATAC-seq

value: Vehicle


title: Single granulosa cell(LCM, DRaqL - Smart-seq2) IL01_SS2_LCMPair05_S13

description: DRaqL - Smart-seq2

value: Ovary

value: LCM

value: Granulosa cell

value: Neighboring


title: WT_4-OHT_1


title: Single oocyte (DRaqL - SC3-seq) Oocyte_09_Sec1_S17

description:
DRaqL - SC3-seq
Oocyte_09_Sec1_S17

data_processing:
After trimming polyA/T sequences, adapter sequences, and poor quality reads, using fastp (v. 0.20.0) and cutadapt (ver. 1.16), the sequenced reads were aligned to the GRCm38 mouse genome assemblywith ERCC spike-in RNA sequences using the HiSAT2 (v. 2.1.0).
Best-matched reads on annotated genes were counted using HTSeq 0.10.0 with a modified GRCm38 gtf file which is extended up to 10 Kb downstream from transcription termination sites of reference genes.
Mapped reads on exons and exon-exon junctions were counted by featureCounts (v2.0.1) with the GRCm38 gtf file and the option "-J" "-p" "-M" "-O" "-t　exon" "-g　transcript_id".
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene, exon and exon-exon junction counts for every sample.

source_name: Oocyte

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in a medium containing 2iLIF [GSK inhibitor (CHIR99021; 3 µM), MEK inhibitor (PD0325901; 0.4 µM), and LIF (1 U/µL) (2iLIF)]

extract_protocol:
Cells were isolated with LCM in 6.4 μL of cell lysis buffer (1× GeneAmp PCR Buffer II [Thermo Fisher], 1.5 mM MgCl2 [Thermo Fisher], 0.5% sodium deoxycholate [SDc] [Nacalai Tesque], and 5 mM dithiothreitol [DTT] [Thermo Fisher] dissolved in deionized distilled water [Gibco] containing 4 U RNaseOUT [Thermo Fisher], 0.4 U porcine liver RNase inhibitor [Takara Bio], 0.05 mM dNTPs [Takara Bio], ERCC RNA Spike-In Mix 1 [Thermo Fisher], and 1.6 ng V1[dT]24 primer ) in the caps of PCR tubes, and spun down into the tubes by brief centrifugation.  Cells were then lysed at 70°C for 6 min, followed by the addition of 2.8 µL quenching buffer (25% Triton X-100 [Nacalai Tesque] and 1% bovine serum albumin [BSA] [Takara Bio]) and incubation at 70°C for 90 sec to quench the denaturing activity of SDc.
The cDNA synthesis and amplification onward were performed as described previously with minor modifications [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. In brief, the first-strand cDNA was synthesized by SuperScript III [Thermo Fisher] and incubating at 50℃  for 5 min followed by heat inactivation at 70℃  for 10 min.  The excess RT primers were degraded by exonuclease I and incubating at 37℃ for 30 min followed by heat inactivation at 80℃ for 25 min. The first-strand cDNA product was poly dA-tailed by TdT and incubating at 37℃  for 1 min followed by heat inactivation at 70℃ for 10 min. Second-strand cDNA synthesis were performed by adding 9.5 μL reaction mixture of ExTaq, Hot Start version [Takara Bio] and V3[dT]24 primer in the ExTaq buffer with the following thermal cycling program (95℃  for 3 min, 50℃  for 2 min, and 72℃  for 3 min). cDNA amplification was performed by addingthe mixture of V1[dT]24 and ExTaq, Hot Start version [Takara Bio] in the ExTaq buffer with the following thermal cycling program (95℃  for 1 min; 20 cycles of 95℃  for 30 sec, 67℃  for 1 min and 72℃  for 3 min with a 6 sec elongation per cycle; and 72℃  for 10 min).  The amplified cDNA was purified with a 0.6× volume of AxyPrep MAG PCR clean-up reagent (Axygen) according to the manufacturer's instructions. Preparation of the libraries for SC3-seq was performed essentially as previously described (Nakamura et al., 2015)(Nakamura et al., 2017).  For Y-adapter sequencing, single-cell cDNAs were pre-amplified using the primers (V3[dT]24, V1[dT]24) and ExTaq HS with the thermal cycling program (95℃  for 3 min; 4 cycles of 95°C for 30 sec, 67℃  for 1 min and 72℃  for 5 min; 72℃  for 10 min). Pre-amplified cDNAs were then subjected to the primer-dimer removal, sonication, end polishing, and the size selection as in SC3-seq. Then, purified cDNA was dA-tailed in a 10 μL dA tailing mixture with incubation at 72℃  for 10 min. The dA-tailed product was subjected to the Y-shaped adaptor ligation by adding a mixture of Y-adaptor and NEB Next Quick Ligation Reaction Buffer and incubating at 20℃  for 15 min and at 72℃  for 20 min. The ligation product was purified with a 0.9×volume of AxyPrep reagent, and subjected to additional PCR amplification in 20 μL with the thermal cycling program (95℃  for 3 min, 55℃  for 1 min, and 72℃  for 1 min; 11 cycles of 95℃  for 30 sec, 60℃  for 1 min, and 72℃  for 1 min; and 72℃  for 3 min), followed by DNA purification with a 0.9×volume of AxyPrep reagent.

treatment_protocol: Mouse ovaries were excised from 8-week-old female mice and snap-frozen in liquid N2. Then, the frozen ovaries were sunk in 10% PVA in cryomolds, and again frozen in liquid N2. The embedded ovaries were sectioned using a CM1860UV cryostat at a thickness of 15 μm, dried at room temperature for more than 1 h, fixed and stained with 1% cresyl violet acetate dissolved in 50% isopropanol, washed with 100% isopropanol, and dried for more than 1 h. Cells in the frozen sections were isolated using a laser microdissection system PALM MB4 (Zeiss).

tag: collecting conditions

tag: class

tag: analysis target

value: gene expression


title: Single oocyte (DRaqL - SC3-seq) Oocyte_08_Sec1_S15

description:
DRaqL - SC3-seq
Oocyte_08_Sec1_S15


title: Single oocyte (DRaqL - SC3-seq) Oocyte_06_Sec2_S12

description:
DRaqL - SC3-seq
Oocyte_06_Sec2_S12


title: Single oocyte (DRaqL - SC3-seq) Oocyte_07_Sec1_S13

description:
DRaqL - SC3-seq
Oocyte_07_Sec1_S13


title: Single oocyte (DRaqL - SC3-seq) Oocyte_06_Sec1_S11

description:
DRaqL - SC3-seq
Oocyte_06_Sec1_S11


title: Single oocyte (DRaqL - SC3-seq) Oocyte_04_Sec2_S8

description:
DRaqL - SC3-seq
Oocyte_04_Sec2_S8


title: Single oocyte (DRaqL - SC3-seq) Oocyte_03_Sec2_S6

description:
DRaqL - SC3-seq
Oocyte_03_Sec2_S6


title: Single oocyte (DRaqL - SC3-seq) Oocyte_02_Sec2_S4

description:
DRaqL - SC3-seq
Oocyte_02_Sec2_S4


title: Single oocyte (DRaqL - SC3-seq) Oocyte_03_Sec1_S5

description:
DRaqL - SC3-seq
Oocyte_03_Sec1_S5


title: WT_4-OHT_2


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_07_Nei_S37

description:
DRaqL - SC3-seq
GCs_10C_07_Nei_S37

source_name: Granulosa cell


title: Single oocyte (DRaqL - SC3-seq) Oocyte_01_Sec2_S2

description:
DRaqL - SC3-seq
Oocyte_01_Sec2_S2


title: CD4+ FOXP3+ Treg, vehicle, spleen, biol rep 2

description: ATAC-seq


title: Single oocyte (DRaqL - SC3-seq) Oocyte_08_Sec2_S16

description:
DRaqL - SC3-seq
Oocyte_08_Sec2_S16


title: Single oocyte (DRaqL - SC3-seq) Oocyte_07_Sec2_S14

description:
DRaqL - SC3-seq
Oocyte_07_Sec2_S14


title: NSD2

city: Chongqing

first: Peng

last: Gao

state: Chongqing

address: 10 Chang Jiang Zhi Lu

country: China

institute: Daping hospital, Army Medical University

data_processing:
Sub-pixel Registration software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM   v1.2.8   was used for fpkm calculation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

growth_protocol: 6-week-old male mice

extract_protocol:
After the liver is taken out of the living body, rinse with 0.9% saline immedietely to remove blood stains and dirt, remove connective tissue and adipose tissue and other tissue types that are not required for research, and absorb the liquid on the surface of the material; divide the tissue sample with a clean blade into a small piece of about 50 mg (about the size of a soybean), after quick freezing in liquid nitrogen, put it into a clean preservation tube with a screw cap. Storing in a refrigerator at minus eighty degrees and shipping on dry ice. And RNA was harvested using Trizol reagent.Total RNA was extracted from the tissues using Trizol(Invitrogen, Carlsbad, CA, USA) accordingto manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. Themix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into anew EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upperaqueous phase where RNA remained was transferred into a new tube with equal volume ofsupernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. Afterdeserting the supernatant, the RNA pellet was washed twice with 1 mL75% ethanol, then the mixwas centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by thepellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treatedwater was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified usinga Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmentedinto small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA wasgenerated using random hexamer-primed reverse transcription, followed by a second-strand cDNAsynthesis. afterwards, A-Tailing Mix and RNA Index Adapters were addedby incubating to endrepair. The cDNA fragments obtained from previous step were amplified by PCR, and productswere purified by Ampure XP Beads, then dissolved in EB solution. The product was validated onthe Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR productsfrom previous step were heated denatured and circularized by the splint oligo sequence to get thefinal library. The single strand circle DNA (ssCir DNA) was formatted as the final library. Thefinal library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300copies of one molecular, DNBs were loaded into the patterned nanoarray andsingleend50basesreads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Mice were fed with high salt diet (HSD, containing 8% NaCl) or normal salt diet (NSD, containing 0.4% NaCl) for 4 months.

value: liver

tag: age

value: post natal month 6

tag: Sex

value: male

value: wild type

value: post normal salt diet weeks 8


title: HSD1

value: post high salt diet weeks 8


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_04_Non_S32

description:
DRaqL - SC3-seq
GCs_10C_04_Non_S32

value: Non-neighboring


title: Single oocyte (DRaqL - SC3-seq) Oocyte_04_Sec1_S7

description:
DRaqL - SC3-seq
Oocyte_04_Sec1_S7

value: Secondary-antral


title: Single oocyte (DRaqL - SC3-seq) Oocyte_02_Sec1_S3

description:
DRaqL - SC3-seq
Oocyte_02_Sec1_S3


title: Single oocyte (DRaqL - SC3-seq) Oocyte_01_Sec1_S1

description:
DRaqL - SC3-seq
Oocyte_01_Sec1_S1


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_03_Nei_S29

description:
DRaqL - SC3-seq
GCs_10C_03_Nei_S29


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_07_Non_S38

description:
DRaqL - SC3-seq
GCs_10C_07_Non_S38


title: HSD2


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_06_Nei_S35

description:
DRaqL - SC3-seq
GCs_10C_06_Nei_S35


title: NSDSIRT3KO2


title: HSDWT3


title: Single oocyte (DRaqL - SC3-seq) Oocyte_09_Sec2_S18

description:
DRaqL - SC3-seq
Oocyte_09_Sec2_S18


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_05_Non_S34

description:
DRaqL - SC3-seq
GCs_10C_05_Non_S34


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_01_Non_S26

description:
DRaqL - SC3-seq
GCs_10C_01_Non_S26


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_05_Nei_S33

description:
DRaqL - SC3-seq
GCs_10C_05_Nei_S33


title: NSDWT2


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_03_Non_S30

description:
DRaqL - SC3-seq
GCs_10C_03_Non_S30


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_04_Nei_S31

description:
DRaqL - SC3-seq
GCs_10C_04_Nei_S31


title: HSDSIRT3KO1


title: NSDWT1


title: NSDSIRT3KO3


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_02_Non_S28

description:
DRaqL - SC3-seq
GCs_10C_02_Non_S28


title: Bulk granulosa cells (DRaqL - SC3-seq) bGCs_02_S42

description:
DRaqL - SC3-seq
bGCs_02_S42

value: Bulk granulosa cells


title: HSDWT2


title: wild type, W7.5 spikelet, replicate 2

city: Shanghai

first: Jin

last: Shi

address: NO 800, Dongchuan Rd

institute: Shanghai Jiaotong University

data_processing:
Trimmomatic was used to clean adapters and low quality reads
Clean reads were aligned to the reference Genome Morex V3 in barley
Transcript levels calculated as fragments per kilobase million (FPKM) using RSEM (v1.3.3).
Assembly: Morex V3 in barley
Supplementary files format and content: All_samples.GeneExpression.FPKM.txt

organism: Hordeum vulgare

source_name: spikelet

extract_protocol:
RNA was isolated using TRIzol Universal Reagent (Tiangen)
library construction was conducted by BGI China

value: spikelet

tag: Stage

value: normal growth


title: wild type, W7.5 spikelet, replicate 3


title: Bulk granulosa cells (DRaqL - SC3-seq) bGCs_01_S41

description:
DRaqL - SC3-seq
bGCs_01_S41


title: NSDSIRT3KO1


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_06_Non_S36

description:
DRaqL - SC3-seq
GCs_10C_06_Non_S36


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_02_Nei_S27

description:
DRaqL - SC3-seq
GCs_10C_02_Nei_S27


title: barley with mads1 knockout, W7.5 spikelet, replicate 3


title: 10 granulosa cells (DRaqL - SC3-seq) GCs_10C_01_Nei_S25

description:
DRaqL - SC3-seq
GCs_10C_01_Nei_S25


title: NSDWT3


title: barley with mads1 knockout, W7.5 spikelet, replicate 1


title: Bulk granulosa cells (DRaqL - SC3-seq) bGCs_08_S48

description:
DRaqL - SC3-seq
bGCs_08_S48


title: HSDWT1


title: HSDSIRT3KO3


title: Bulk granulosa cells (DRaqL - SC3-seq) bGCs_06_S46

description:
DRaqL - SC3-seq
bGCs_06_S46


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL11_20_S6_IL10

description:
DRaqL - Smart-seq2
IL10_SmSeq2DRaqL11_20_S6

extract_protocol:
Cells were isolated with LCM in 6.4 μL of cell lysis buffer (0.6 μL of 5× SuperScript II buffer, 0.1 μL of 100 μM Oligo dT VN, 0.8 μL of dNTP mix [25 mM each], 0.25 μL of 40 U/μL recombinant RNase inhibitor [Takara Bio], 0.5 μL of 100 mM DTT, 0.06 μL of 1 M MgCl2 [Sigma-Aldrich], 2 μL of 5 M Betaine [Sigma-Aldrich], 0.16 μL of 1:500,000 diluted ERCC RNA Spike-In Mix 1, 0.4 μL of 5% SDc, and 1.53 μL of DDW) in the caps of PCR tubes, and spun down into the tubes by brief centrifugation.  The isolated cells were lysed at 72°C for 6 min, followed by addition of 2.8 μL quenching buffer (0.7 μL of Triton X-100, 0.7 μL of 2% BSA, and 1.4 μL of 5× SuperScript II buffer [Thermo Fisher]).  Then, 1.6 μL of a template-switching mixture (0.1 μL of 100 μM N-template-switching oligo, 0.25 μL of SuperScript II, 0.25 μL of SuperScript III, 0.2 μL of recombinant RNase inhibitor, and 0.8 μL of DDW) was added, followed by the cycling RT program for DRaqL-Smart-seq2.  Then, cDNA amplification was performed by adding 15 μL of Seq amp PCR mixture (12.5 μL of 2x SeqAmp buffer (Takara Bio), 0.05 μL of 100 μM N-IS PCR primer, 0.5 μL of SeqAmp DNA polymerase (Takara Bio), and 1.95 μL of DDW) and applying the SeqAmp thermal cycling program.  For oocytes, we used a PCR program of 18 cycles.  The amplified cDNA (25.8 μL) was purified with a 0.8× volume of AxyPrep MAG PCR clean-up reagent according to the manufacturer’s instructions.
The cDNA synthesis and amplification onward were performed as described previously with minor modifications [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. In brief, the first-strand cDNA was synthesized by SuperScript III [Thermo Fisher] and incubating at 50℃  for 5 min followed by heat inactivation at 70℃  for 10 min.  The excess RT primers were degraded by exonuclease I and incubating at 37℃ for 30 min followed by heat inactivation at 80℃ for 25 min. The first-strand cDNA product was poly dA-tailed by TdT and incubating at 37℃  for 1 min followed by heat inactivation at 70℃ for 10 min. Second-strand cDNA synthesis were performed by adding 9.5 μL reaction mixture of ExTaq, Hot Start version [Takara Bio] and V3[dT]24 primer in the ExTaq buffer with the following thermal cycling program (95℃  for 3 min, 50℃  for 2 min, and 72℃  for 3 min). cDNA amplification was performed by addingthe mixture of V1[dT]24 and ExTaq, Hot Start version [Takara Bio] in the ExTaq buffer with the following thermal cycling program (95℃  for 1 min; 20 cycles of 95℃  for 30 sec, 67℃  for 1 min and 72℃  for 3 min with a 6 sec elongation per cycle; and 72℃  for 10 min).  The amplified cDNA was purified with a 0.6× volume of AxyPrep MAG PCR clean-up reagent (Axygen) according to the manufacturer's instructions. Preparation of the libraries for SC3-seq was performed essentially as previously described (Nakamura et al., 2015)(Nakamura et al., 2017).  For Y-adapter sequencing, single-cell cDNAs were pre-amplified using the primers (V3[dT]24, V1[dT]24) and ExTaq HS with the thermal cycling program (95℃  for 3 min; 4 cycles of 95°C for 30 sec, 67℃  for 1 min and 72℃  for 5 min; 72℃  for 10 min). Pre-amplified cDNAs were then subjected to the primer-dimer removal, sonication, end polishing, and the size selection as in SC3-seq. Then, purified cDNA was dA-tailed in a 10 μL dA tailing mixture with incubation at 72℃  for 10 min. The dA-tailed product was subjected to the Y-shaped adaptor ligation by adding a mixture of Y-adaptor and NEB Next Quick Ligation Reaction Buffer and incubating at 20℃  for 15 min and at 72℃  for 20 min. The ligation product was purified with a 0.9×volume of AxyPrep reagent, and subjected to additional PCR amplification in 20 μL with the thermal cycling program (95℃  for 3 min, 55℃  for 1 min, and 72℃  for 1 min; 11 cycles of 95℃  for 30 sec, 60℃  for 1 min, and 72℃  for 1 min; and 72℃  for 3 min), followed by DNA purification with a 0.9×volume of AxyPrep reagent.


title: HSDSIRT3KO2


title: Bulk granulosa cells (DRaqL - SC3-seq) bGCs_05_S45

description:
DRaqL - SC3-seq
bGCs_05_S45


title: Bulk granulosa cells (DRaqL - SC3-seq) bGCs_04_S44

description:
DRaqL - SC3-seq
bGCs_04_S44


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL10

description:
LCM-seq
IL10_LCMseq31_40_S4

extract_protocol:
Smart-seq2 cDNA amplification was performed as described (6), except for the volume of cell lysis solution.  Briefly, cells were isolated with LCM in 6.4 μL cell lysis solution (1 μL of 10 μM Oligo dT VN, 1 μL of dNTPs mix [10 mM each], 0.21 μL of 40 U/μL Recombinant RNase inhibitor, 0.17 μL of 5% Triton X-100, 0.16 μL of 1:500,000 diluted ERCC RNA Spike-In Mix 1, and 3.86 μL of DDW) in the caps of PCR tubes, and spun down into the tubes by brief centrifugation.  The isolated cells were lysed at 72°C for 3 min, and were put on ice immediately after the cell lysis.  Then, 5.45 μL of reverse transcription mixture (2 μL of 5× SuperScript II buffer, 0.5 μL of 100 mM DTT, 2 μL of 5 M Betaine, 0.1 μL of 1 M MgCl2, 0.25 μL of 40 U/μL Recombinant RNase inhibitor, 0.1 μL of 100 μM template-switching oligo, and 0.5 μL of SuperScript II) was added to the tube, followed by cycling RT program for Smart-seq2.  Then, cDNA amplification was performed by adding 15 μL of KAPA PCR mixture (12.5 μL of 2× KAPA HiFi HotStart ReadyMix, 0.2 μL of 10 μM IS PCR primer, 2.3 μL of DDW), and applying the HiFi thermal cycling program.
The cDNA synthesis and amplification onward were performed as described previously with minor modifications [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. In brief, the first-strand cDNA was synthesized by SuperScript III [Thermo Fisher] and incubating at 50℃  for 5 min followed by heat inactivation at 70℃  for 10 min.  The excess RT primers were degraded by exonuclease I and incubating at 37℃ for 30 min followed by heat inactivation at 80℃ for 25 min. The first-strand cDNA product was poly dA-tailed by TdT and incubating at 37℃  for 1 min followed by heat inactivation at 70℃ for 10 min. Second-strand cDNA synthesis were performed by adding 9.5 μL reaction mixture of ExTaq, Hot Start version [Takara Bio] and V3[dT]24 primer in the ExTaq buffer with the following thermal cycling program (95℃  for 3 min, 50℃  for 2 min, and 72℃  for 3 min). cDNA amplification was performed by addingthe mixture of V1[dT]24 and ExTaq, Hot Start version [Takara Bio] in the ExTaq buffer with the following thermal cycling program (95℃  for 1 min; 20 cycles of 95℃  for 30 sec, 67℃  for 1 min and 72℃  for 3 min with a 6 sec elongation per cycle; and 72℃  for 10 min).  The amplified cDNA was purified with a 0.6× volume of AxyPrep MAG PCR clean-up reagent (Axygen) according to the manufacturer's instructions. Preparation of the libraries for SC3-seq was performed essentially as previously described (Nakamura et al., 2015)(Nakamura et al., 2017).  For Y-adapter sequencing, single-cell cDNAs were pre-amplified using the primers (V3[dT]24, V1[dT]24) and ExTaq HS with the thermal cycling program (95℃  for 3 min; 4 cycles of 95°C for 30 sec, 67℃  for 1 min and 72℃  for 5 min; 72℃  for 10 min). Pre-amplified cDNAs were then subjected to the primer-dimer removal, sonication, end polishing, and the size selection as in SC3-seq. Then, purified cDNA was dA-tailed in a 10 μL dA tailing mixture with incubation at 72℃  for 10 min. The dA-tailed product was subjected to the Y-shaped adaptor ligation by adding a mixture of Y-adaptor and NEB Next Quick Ligation Reaction Buffer and incubating at 20℃  for 15 min and at 72℃  for 20 min. The ligation product was purified with a 0.9×volume of AxyPrep reagent, and subjected to additional PCR amplification in 20 μL with the thermal cycling program (95℃  for 3 min, 55℃  for 1 min, and 72℃  for 1 min; 11 cycles of 95℃  for 30 sec, 60℃  for 1 min, and 72℃  for 1 min; and 72℃  for 3 min), followed by DNA purification with a 0.9×volume of AxyPrep reagent.


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL10

description:
LCM-seq
IL10_LCMseq21_30_S3


title: UC3

city: Qingdao

first: Mei-Yan

last: Liu

state: Shandong

address: Aoshanwei Street

institute: Shandong university

description: Urea-N

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads need to be filtered by quality.
Trimmomatic software was first used for quality control and linker removal, and then low-quality bases and N-bases or low-quality reads were filtered out.
Finally, we got high-quality clean reads.
Using Rockhooper2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Microcystis aeruginosa FACHB-905 = DIANCHI905

source_name: prokaryotic cell

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or other platform) and 150 bp/125bp paired-end reads were generated.

value: FACHB-905 = DIANCHI905

value: prokaryotic cell

value: WT

value: Urea-N


title: barley with mads1 knockout, W7.5 spikelet, replicate 2


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL10

description:
LCM-seq
IL10_LCMseq01_10_S1

value: LCM


title: wild type, W7.5 spikelet, replicate 1


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL10

description:
DRaqL - Smart-seq2
IL10_SmSeq2DRaqL31_40_S8

value: gene expression


title: UC2

description: Urea-N


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL21_30_S7_IL10

description:
DRaqL - Smart-seq2
IL10_SmSeq2DRaqL21_30_S7


title: UT2


title: Bulk granulosa cells (DRaqL - SC3-seq) bGCs_03_S43

description:
DRaqL - SC3-seq
bGCs_03_S43


title: UC1

description: Urea-N


title: UT1


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL11_20_S6_IL09

description:
DRaqL - Smart-seq2
IL09_SmSeq2DRaqL11_20_S6


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL09

description:
DRaqL - Smart-seq2
IL09_SmSeq2DRaqL31_40_S8


title: NC3

description: nitrate-N

value: nitrate-N


title: UT3


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL10

description:
DRaqL - Smart-seq2
IL10_SmSeq2DRaqL01_10_S5


title: NT3


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL09

description:
LCM-seq
IL09_LCMseq21_30_S3


title: NC1

description: nitrate-N


title: VLD_CV55

type: genomic

city: BETHESDA

first: Rust

last: Turakulov

state: MD

address: 10 Central rd

department: NCI

institute: NIH

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R packages: meffil, minfi

label_protocol: Illumina beachip kit and standard protocol

extract_protocol: DNA was extracted from FFPE tissue with  Qiagen DNA extraction kit and followed with Illumina restotation kit.

tag: disease state

value: Medulloblastoma, grade 4

value: Female

value: FFPE

value: Brain, left cerebellar pontine mass


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL09

description:
LCM-seq
IL09_LCMseq11_20_S2


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL21_30_S7_IL09

description:
DRaqL - Smart-seq2
IL09_SmSeq2DRaqL21_30_S7


title: NT2


title: VLD_CV54

value: Diffuse pediatric-type high-grade glioma

value: Brain, right frontal


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL09

description:
LCM-seq
IL09_LCMseq01_10_S1

value: Non-neighboring


title: VLD_CV53

value: Medulloblastoma, non-WNT/non-SHH

value: Male

value: Brain, posterior fossa, CP angle


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL09

description:
DRaqL - Smart-seq2
IL09_SmSeq2DRaqL01_10_S5


title: NT1

value: FACHB-905 = DIANCHI905


title: VLD_CV52

value: Choroid Glioma

value: Brain, third ventricular


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL09

description:
LCM-seq
IL09_LCMseq31_40_S4


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL10

description:
LCM-seq
IL10_LCMseq11_20_S2


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL21_30_S7_IL08

description:
DRaqL - Smart-seq2
IL08_SmSeq2DRaqL21_30_S7


title: VLD_CV51

value: High-grade glioma (astrocytoma), grade 3-4

value: Brain, right frontal lobe


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL11_20_S6_IL08

description:
DRaqL - Smart-seq2
IL08_SmSeq2DRaqL11_20_S6

value: LCM

value: gene expression


title: VLD_CV50

value: High-grade glioma

value: Brain, left temporal tumor


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL08

description:
DRaqL - Smart-seq2
IL08_SmSeq2DRaqL01_10_S5


title: VLD_CV46

value: DLGNT vs. PA

value: FFPE

value: Cervical spine


title: VLD_CV47

value: Pilocytic astrocytoma

value: Female

value: Brain, suprasellar


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL08

description:
LCM-seq
IL08_LCMseq31_40_S4

value: Non-neighboring


title: NC2

description: nitrate-N

value: prokaryotic cell

value: WT

value: nitrate-N


title: VLD_CV45

value: Left craniotomy for tumor resection

value: Male

value: Brain


title: VLD_CV49

value: Meningioma, WHO grade G3

value: Brain, left parasagittal


title: VLD_CV48

value: Glioma with mitoses


title: VLD_CV43

value: Meningioma, meningothelial subtype

value: Brain, meninges, right sphenoid wing


title: VLD_CV44

value: Dysembryoplastic neuroepithelial tumor

value: FFPE

value: Brain, left parietal lobe


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL07

description:
DRaqL - Smart-seq2
IL07_SmSeq2DRaqL31_40_S8

value: LCM

value: gene expression


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL08

description:
LCM-seq
IL08_LCMseq01_10_S1

value: Non-neighboring


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL08

description:
LCM-seq
IL08_LCMseq11_20_S2


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL21_30_S7_IL07

description:
DRaqL - Smart-seq2
IL07_SmSeq2DRaqL21_30_S7


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL07

description:
DRaqL - Smart-seq2
IL07_SmSeq2DRaqL01_10_S5


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL08

description:
DRaqL - Smart-seq2
IL08_SmSeq2DRaqL31_40_S8


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL11_20_S6_IL07

description:
DRaqL - Smart-seq2
IL07_SmSeq2DRaqL11_20_S6


title: VLD_CV41

value: Atypical teratoid/rhabdoid tumor

value: Female

value: Brain, posterior fossa


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL07

description:
LCM-seq
IL07_LCMseq11_20_S2


title: FAW S3

city: Daejeon

first: Rashmi

middle: Manohar

last: Mahalle

address: Yuseong-gu

country: South Korea

institute: Chungnam National Unversity

data_processing:
The trimmed reads were aligned to the miRNA precursors of s. frugiperda, P. xylostella, and B. mori in miRbase R.22. using miRDeep2. Only tags matching exactly with the mature 5’ or 3’ regions of three previously annotated species miRNAs  were accepted as known miRNAs and retained for further analysis. Unannotated clean sequences that did not match the above databases were further used to analyse and predict novel miRNAs using the miRDeep2 software.
Assembly: ZJU_sfru_1.0
Supplementary files format and content: raw_counts.xlsx

organism: Spodoptera frugiperda

source_name: whole animal

extract_protocol:
Total RNA extraction using the Qiagen miRNeasy Mini Kit, according to the manufacturer’s instructions (Qiagen, Valencia, CA)
Qualified total RNA was used to construct sRNA libraries using the Truseq small RNA sample Pre Kit (Illumina).Illumina sRNA libraries were constructed from each pool, and 50-bp single-end (sE50) sequence read data were generated on an Illumina Hiseq 4000 at the Research Technology support Facility (Michigan state University, East Lancing, MI, UsA). Clean reads were obtained from the raw data after processing adapters, low-quality reads, and sequences of fewer than 18 nucleotides using cutadapt v.3.471.

value: susceptible

value: whole animal


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL06

description:
DRaqL - Smart-seq2
IL06_SmSeq2DRaqL31_40_S8


title: VLD_CV42

value: GBM

value: Brain


title: VLD_CV40

value: Astrocytoma with foci with high-grade features, consider HGAP

value: Brain, fourth ventricle


title: FAW S1


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL07

description:
LCM-seq
IL07_LCMseq21_30_S3


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL08

description:
LCM-seq
IL08_LCMseq21_30_S3


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL07

description:
LCM-seq
IL07_LCMseq01_10_S1


title: FAW S2


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL06

description:
DRaqL - Smart-seq2
IL06_SmSeq2DRaqL01_10_S5


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL06

description:
LCM-seq
IL06_LCMseq31_40_S4


title: FAW R2

value: resistant


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL06

description:
LCM-seq
IL06_LCMseq21_30_S3


title: FAW R1


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL07

description:
LCM-seq
IL07_LCMseq31_40_S4


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL06

description:
LCM-seq
IL06_LCMseq11_20_S2


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL05

description:
DRaqL - Smart-seq2
IL05_SmSeq2DRaqL31_40_S8

value: Neighboring


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL11_20_S6_IL05

description:
DRaqL - Smart-seq2
IL05_SmSeq2DRaqL11_20_S6


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL21_30_S7_IL05

description:
DRaqL - Smart-seq2
IL05_SmSeq2DRaqL21_30_S7


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL05

description:
DRaqL - Smart-seq2
IL05_SmSeq2DRaqL01_10_S5


title: FAW R3


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL21_30_S7_IL06

description:
DRaqL - Smart-seq2
IL06_SmSeq2DRaqL21_30_S7


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL05

description:
LCM-seq
IL05_LCMseq31_40_S4


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL05

description:
LCM-seq
IL05_LCMseq11_20_S2


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL21_30_S7_IL04

description:
DRaqL - Smart-seq2
IL04_SmSeq2DRaqL21_30_S7


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL11_20_S6_IL04

description:
DRaqL - Smart-seq2
IL04_SmSeq2DRaqL11_20_S6


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL05

description:
LCM-seq
IL05_LCMseq21_30_S3


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL06

description:
LCM-seq
IL06_LCMseq01_10_S1


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL04

description:
DRaqL - Smart-seq2
IL04_SmSeq2DRaqL31_40_S8


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL04

description:
LCM-seq
IL04_LCMseq21_30_S3


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL04

description:
LCM-seq
IL04_LCMseq11_20_S2


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL04

description:
LCM-seq
IL04_LCMseq01_10_S1


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL03

description:
DRaqL - Smart-seq2
IL03_SmSeq2DRaqL31_40_S8


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL03

description:
DRaqL - Smart-seq2
IL03_SmSeq2DRaqL01_10_S5


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL03

description:
LCM-seq
IL03_LCMseq31_40_S4


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL03

description:
LCM-seq
IL03_LCMseq21_30_S3


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL11_20_S6_IL03

description:
DRaqL - Smart-seq2
IL03_SmSeq2DRaqL11_20_S6


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL03

description:
LCM-seq
IL03_LCMseq11_20_S2


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL02

description:
DRaqL - Smart-seq2
IL02_SmSeq2DRaqL31_40_S8


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL03

description:
LCM-seq
IL03_LCMseq01_10_S1


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL02

description:
DRaqL - Smart-seq2
IL02_SmSeq2DRaqL01_10_S5


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL02

description:
LCM-seq
IL02_LCMseq31_40_S4


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL02

description:
LCM-seq
IL02_LCMseq11_20_S2


title: S54D-11

city: Provo

first: Timothy

middle: G

last: Jenkins

state: UT

address: 4005 Life Sciences Building

department: Cell Biology and Physiology

institute: Brigham Young University

description: Somatic Cell Contamination in Sperm

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

data_processing: Data was processed using the minfi R package, and normalized using SWAN normalization.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Samples were extracted using Qiagen DNA extraction kit

tag: gender

value: Male

tag: sample type

value: Sperm and Whole Blood

tag: contamination type

tag: contamination number


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL02

description:
LCM-seq
IL02_LCMseq01_10_S1


title: S54D-1

description: Somatic Cell Contamination in Sperm


title: S54D-12

description: Somatic Cell Contamination in Sperm


title: S54D-9

description: Somatic Cell Contamination in Sperm


title: S54D-8

description: Somatic Cell Contamination in Sperm


title: S54D-6

description: Somatic Cell Contamination in Sperm


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL11_20_S6_IL02

description:
DRaqL - Smart-seq2
IL02_SmSeq2DRaqL11_20_S6


title: PX9K-11

description: Somatic Cell Contamination in Sperm


title: S54D-5

description: Somatic Cell Contamination in Sperm


title: S54D-2

description: Somatic Cell Contamination in Sperm


title: S54D-10

description: Somatic Cell Contamination in Sperm


title: PX9K-12

description: Somatic Cell Contamination in Sperm


title: PX9K-8

description: Somatic Cell Contamination in Sperm


title: S54D-7

description: Somatic Cell Contamination in Sperm


title: Single granulosa cell (LCM-seq) LCMseq21_30_S3_IL01

description:
LCM-seq
IL01_LCMseq21_30_S3


title: PX9K-10

description: Somatic Cell Contamination in Sperm


title: S54D-3

description: Somatic Cell Contamination in Sperm


title: Single granulosa cell (LCM-seq) LCMseq11_20_S2_IL01

description:
LCM-seq
IL01_LCMseq11_20_S2


title: S54D-4

description: Somatic Cell Contamination in Sperm


title: PX9K-6

description: Somatic Cell Contamination in Sperm


title: PX9K-9

description: Somatic Cell Contamination in Sperm


title: PX9K-4

description: Somatic Cell Contamination in Sperm


title: PX9K-7

description: Somatic Cell Contamination in Sperm


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL12

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL12

extract_protocol:
Cells were isolated with LCM in 6.4 μL of cell lysis buffer (0.6 μL of 5× SuperScript II buffer, 0.1 μL of 100 μM Oligo dT VN, 0.8 μL of dNTP mix [25 mM each], 0.25 μL of 40 U/μL recombinant RNase inhibitor, 0.5 μL of 100 mM DTT, 0.06 μL of 1 M MgCl2, 2 μL of 5 M Betaine, 0.4 μL of 5% Triton X-100, 0.32 μL of 900 mAU/mL Qiagen Protease, and 1.37 μL of DDW) in the caps of PCR tubes, and spun down into the tubes by brief centrifugation.  The isolated cells were lysed by protease digestion at 50°C for 10 min and then heat inactivated at 80°C for 15 min, followed by the addition of 0.8 μL of 1:2500,000 diluted ERCC RNA Spike-In Mix 1 and incubation at 72°C for 90 sec.  Then, 3.6 μL of a template-switching mixture (1.4 μL of 5× SuperScript II buffer, 0.1 μL of 100 μM N-template-switching oligo, 0.25 μL of SuperScript II, 0.25 μL of SuperScript III, 0.2 μL of recombinant RNase inhibitor, and 1.4 μL DDW) was added, followed by the cycling RT program for DRaqL-Smart-seq2.  Then, cDNA amplification was performed by adding 15 μL of the SeqAmp PCR mixture, and applying the SeqAmp thermal cycling program.  The amplified cDNA (25.8 μL) was purified with a 0.8× volume of AxyPrep MAG PCR clean-up reagent according to the manufacturer’s instructions.
The cDNA synthesis and amplification onward were performed as described previously with minor modifications [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. In brief, the first-strand cDNA was synthesized by SuperScript III [Thermo Fisher] and incubating at 50℃  for 5 min followed by heat inactivation at 70℃  for 10 min.  The excess RT primers were degraded by exonuclease I and incubating at 37℃ for 30 min followed by heat inactivation at 80℃ for 25 min. The first-strand cDNA product was poly dA-tailed by TdT and incubating at 37℃  for 1 min followed by heat inactivation at 70℃ for 10 min. Second-strand cDNA synthesis were performed by adding 9.5 μL reaction mixture of ExTaq, Hot Start version [Takara Bio] and V3[dT]24 primer in the ExTaq buffer with the following thermal cycling program (95℃  for 3 min, 50℃  for 2 min, and 72℃  for 3 min). cDNA amplification was performed by addingthe mixture of V1[dT]24 and ExTaq, Hot Start version [Takara Bio] in the ExTaq buffer with the following thermal cycling program (95℃  for 1 min; 20 cycles of 95℃  for 30 sec, 67℃  for 1 min and 72℃  for 3 min with a 6 sec elongation per cycle; and 72℃  for 10 min).  The amplified cDNA was purified with a 0.6× volume of AxyPrep MAG PCR clean-up reagent (Axygen) according to the manufacturer's instructions. Preparation of the libraries for SC3-seq was performed essentially as previously described (Nakamura et al., 2015)(Nakamura et al., 2017).  For Y-adapter sequencing, single-cell cDNAs were pre-amplified using the primers (V3[dT]24, V1[dT]24) and ExTaq HS with the thermal cycling program (95℃  for 3 min; 4 cycles of 95°C for 30 sec, 67℃  for 1 min and 72℃  for 5 min; 72℃  for 10 min). Pre-amplified cDNAs were then subjected to the primer-dimer removal, sonication, end polishing, and the size selection as in SC3-seq. Then, purified cDNA was dA-tailed in a 10 μL dA tailing mixture with incubation at 72℃  for 10 min. The dA-tailed product was subjected to the Y-shaped adaptor ligation by adding a mixture of Y-adaptor and NEB Next Quick Ligation Reaction Buffer and incubating at 20℃  for 15 min and at 72℃  for 20 min. The ligation product was purified with a 0.9×volume of AxyPrep reagent, and subjected to additional PCR amplification in 20 μL with the thermal cycling program (95℃  for 3 min, 55℃  for 1 min, and 72℃  for 1 min; 11 cycles of 95℃  for 30 sec, 60℃  for 1 min, and 72℃  for 1 min; and 72℃  for 3 min), followed by DNA purification with a 0.9×volume of AxyPrep reagent.

treatment_protocol: Mouse ovaries were excised from 8-week-old female mice and snap-frozen in liquid N2. Then, the frozen ovaries were sunk in 10% PVA in cryomolds, and again frozen in liquid N2. The embedded ovaries were sectioned using a CM1860UV cryostat at a thickness of 15 μm, dried at room temperature for more than 1 h. Formalin fixation was performed with 10% formalin neutral buffer solution (Wako) at room temperature for 24 h, and the fixed sections were stained with 1% cresyl violet acetate in 50% isopropanol and dried for more than 1 h. Cells in the sections were isolated using a laser microdissection system PALM MB4 (Zeiss).

value: LCM (24 h Formalin-fixed)

value: Secondary-antral


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL01_10_S5_IL01

description:
DRaqL - Smart-seq2
IL01_SmSeq2DRaqL01_10_S5

value: LCM

value: gene expression


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL11

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL11


title: PX9K-1

description: Somatic Cell Contamination in Sperm


title: GD7H-11

description: Somatic Cell Contamination in Sperm


title: PX9K-5

description: Somatic Cell Contamination in Sperm


title: Single granulosa cell (LCM-seq) LCMseq31_40_S4_IL01

description:
LCM-seq
IL01_LCMseq31_40_S4


title: GD7H-10

description: Somatic Cell Contamination in Sperm


title: PKD_tissue_1

city: Jinan

first: liqiang

last: guo

address: No. 107, Wenhua West Road

department: Shandong University

institute: Qilu Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: HISAT2 v2.0.5
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primary kidney cells

extract_protocol:
RNA libaries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: primary kidney cells

value: Tissue


title: PKD_tissue_3


title: PX9K-3

description: Somatic Cell Contamination in Sperm


title: PX9K-2

description: Somatic Cell Contamination in Sperm


title: Single granulosa cell (DRaqL - Smart-seq2) SmSeq2DRaqL31_40_S8_IL01

description:
DRaqL - Smart-seq2
IL01_SmSeq2DRaqL31_40_S8


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL08

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL08


title: PKD_tissue_2


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL09

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL09


title: GD7H-12

description: Somatic Cell Contamination in Sperm


title: Single granulosa cell (LCM-seq) LCMseq01_10_S1_IL01

description:
LCM-seq
IL01_LCMseq01_10_S1


title: GD7H-8

description: Somatic Cell Contamination in Sperm


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL07

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL07


title: organoid_c_p15

value: Organoid


title: organoid_c_p5


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL06

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL06


title: organoid_b_p14


title: organoid_b_p4


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL05

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL05

value: Primary follicle


title: GD7H-4

description: Somatic Cell Contamination in Sperm


title: flk:GFP,injected with MV4-11 derived Evs 2

city: Guangzhou

first: Xinyi

last: Wang

state: Guangdong

address: Guangzhou

institute: SUN YAT-SEN MEMORIAL HOSPITAL

data_processing:
After removing low quality reads and trimming the adaptor sequences by Trim Galore (v0.5.0, Babraham Bioinformatics), RNA-Seq reads were aligned to zebrafish genome GRCz11 by Salmon (v0.03.1, COMBINE-lab) with ENCODE options and genes were annotated by Ensembl database. For expression quantification, the uniquely mapped reads were transformed to counts by Salmon and normalized to counts per million (CPM) or log2(CPM+1) by edgeR (v3.40.1, Bioconductor). The batch effect was removed by sva (v3.46.0, Bioconductor). Three replicates of PBS or EV-treated ECs were aligned by Principal ComponentAnalysis (PCA), and one replicate that was diverged from the other two was removed for the following analysis.
Assembly: GRCz11
Supplementary files format and content: Zebrafish__Raw_Counts.tar with raw counts matrices

organism: Danio rerio

source_name: endothelial cells

extract_protocol:
Five hundred of Tg(flk:GFP) larvae were injected with PBS (control) or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h-post-injection (hpi) before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution (0.5 g/L; T3924; Sigma) with 1,000 μL pipette tip for 20 min. The dissociated cells were then filtered with a 70 μm filter (BD Transduction Laboratories) to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7-AAD (5 μg/mL, BD Transduction Laboratories) on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS (MoFlo XDP, Beckman) and total RNA was extracted with Trizol (15596, Invitrogen) according to the manufacturer’s instructions.
Low input RNA-Seq was performed according to the published protocol with modifications . Briefly, mRNAs were purified by VAHTS RNA Clean Beads (N412, Vayzme) in RNase-free H2O with reverse transcription mix, amplified for 15 cycles, and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads (N411, Vazyme). Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit (Q3285, Guangzhou IGE biotechnology ltd) and verified by DNA gel electrophoresis (1.5-2 kb). Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina (TD503, Vazyme) and adaptor-ligated DNAs (400 bp) were selected by VAHTS DNA Clean Beads (N411, Vazyme). Libraries were sequenced by using NovaSeq-PE150 as 150 bp paired-end.

value: endothelial cells

tag: genotype

value: WT

tag: treatment

value: injected with MV4-11 derived EVs,sorting


title: GD7H-6

description: Somatic Cell Contamination in Sperm


title: flk:GFP,injected with MV4-11 derived Evs 1

tag: cell type


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL04

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL04


title: flk:GFP,injected with MV4-11 derived Evs 3


title: organoid_a_p14


title: flk:GFP,injected with PBS 3

value: injected with PBS,sorting


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL03

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL03


title: flk:GFP,injected with PBS 2


title: organoid_a_p4


title: flk:GFP,injected with PBS 1


title: GD7H-9

description: Somatic Cell Contamination in Sperm


title: PKD_organoid_3


title: GRMut2

city: Sheffield

first: Vincent

middle: Trevor

last: Cunliffe

state: South Yorkshire

address: Western Bank

department: School of Biosciences

country: United Kingdom

institute: University of Sheffield

data_processing:
Adapters and primers were trimmed and reads were quality filtered to phred-quality Q15 and then mapped to the in silico converted reference genome using BISMARK, with Bowtie2 as the aligner.
Sequence alignments were refined by local realignment and recalibration using Bis-SNP adopted GATK modules.
Methylation calls were made using the bismark_methylation_extractor tool of Bismark v0.16.3 with the following parameters: —-bedGraph —-counts —-multicore 4 —-no_overlap
Basecalls performed using CASAVA version 1.8.2
Genome_build: drer10.85
Supplementary_files_format_and_content: The BedGraph coverage files were generated using Bismark. The .cov file gives the methylation level of each CpG. The column headings are as follows: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>.

source_name: Brain

extract_protocol:
Whole brains were dissected and genomic DNA was extracted using Qiagen Dneasy Blood and Tissue Kit (Cat No./ID: 69504) according to the manufacturer's instructions.
Library prep protocol was optimised at GATC Biotech based on the NEBNext Ultra I DNA Lib Prep Kit for Illumina. This included: fragmentation by sonication, end repair, a-tailing, ligation of methylated adapters, bisulfite conversion, index PCR, size selection by extraction from agarose gel (band at ~350 bp)

tag: tissue

value: Brain

tag: developmental stage

value: Adult


title: GRMut3


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL01

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL01


title: GRWT3


title: GD7H-3

description: Somatic Cell Contamination in Sperm


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL02

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL02


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL12

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL12

value: Non-neighboring


title: PKD_organoid_1

tag: strain


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL11

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL11

tag: collecting conditions


title: Library8c DNA-seq

description: DNA-seq on reporter gene barcode amplicons from plasmid DNA library

organism: Escherichia coli

extract_protocol:
RNA was extracted from retinas with TRIzol and treated with Turbo Dnase. cDNA was prepared using SuperScript IV.
Sequence barcodes from reporter genes were amplified by PCR and purified with Monarch PCR cleanup kit. Custom Illumina adapters were added by PCR.

tag: cell line

value: wild-type


title: GRWT2


title: SI_N8

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
bulk RNA-seq
full-length gene expression
Smart-seq2

data_processing:
For RNA-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3.
genome build: mm10
processed data files format and content: TPM expression matrix files were extracted from RSEM gene-results and initially filtered for expressed protein-coding genes.
processed data files format and content: TPM expression matrix files were extracted from RSEM gene-results and initially filtered for expressed protein-coding genes.

source_name: Small Intestine

growth_protocol: primary eosinophils

extract_protocol:
RNA were extracted from cells using AMPure XP beads (Backman)
Full-length Smart-seq2 and 10x genomics scRNA-seq

treatment_protocol: The mice were at the steady state

value: Small Intestine

value: Nmur1- Eosinophils

value: NMUR1-TdT reporter

value: 8-12 weeks

value: pooled male and female


title: Library8b DNA-seq

data_processing:
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified using custom python scripts.
Demultiplexed reads were used to determine the read counts for each barcode with custom python scripts.
To obtain barcode read counts, reads were matched to barcoded reporter gene sequences using custom python scripts. Only exact barcoded matches were counted. FASTA files with reporter gene sequences for each library are included as supplementary files.
Assembly: mm10
Supplementary files format and content: Each sample has its own tab-delimited file. Column 1: Barcode sequence. Column 2: cis-regulatory element name. Column 3: Barcode counts.


title: Library8a DNA-seq


title: PKD_organoid_2

value: primary kidney cells


title: tissue_c_

value: Tissue


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL10

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL10

value: LCM (24 h Formalin-fixed)

tag: class

tag: analysis target

value: gene expression


title: GD7H-2

description: Somatic Cell Contamination in Sperm

value: Male

value: Sperm and Whole Blood


title: GD7H-1

description: Somatic Cell Contamination in Sperm


title: EX8V-9

description: Somatic Cell Contamination in Sperm


title: EX8V-12

description: Somatic Cell Contamination in Sperm


title: SI_N5

tag: age

tag: Sex


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL09

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL09


title: SI_N4


title: tissue_a


title: SI_N3


title: EX8V-11

description: Somatic Cell Contamination in Sperm


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL08

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL08


title: HEK293 cells, NONOTFE3mRuby2 (NE), biological rep 2

city: Indianapolis

first: Ricardo

last: Cordova

state: IN

address: 635 Barnhill Drive, MS4067

institute: Indiana University School of Medicine

data_processing:
Adaptor sequences were removed from raw fastq data files using cutadapt and aligned to human reference genome GRCh38 using HISAT2.
Number of reads for each transcript was determined by using FeatureCounts from the Subread package.
DESeq2 R-package was used to determine differential gene expression.
Assembly: GRCh38/hg38
Supplementary files format and content: cvs file. Data matrix for all samples

growth_protocol: HEK293 cells were culture in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. All cell lines were maintained at 37°C in a fully humidified atmosphere containing 5% CO2, used at early passage for experiments, and tested to be free of mycoplasma contamination.

extract_protocol:
Total RNA was extracted from using a RNeasy Plus Kit (Qiagen, Cat. #74034) according to the manufacturer’s instructions.
RNA quality control, library preparation, and NGS paired-end sequencing on Illumina HiSeq platform were carried out at GeneWiz (South Plainfield, NJ).

treatment_protocol: HEK293 were transfected with plasmids expressing mRuby2, SFPQmRuby2, NONOmRuby2, PRCCmRuby2, TFE3mRuby2, PRCCTFE3mRuby2, SFPQTFE3mRuby2 or NONOTFE3mRuby2.

value: Immortalized human embryonic kidney cells


title: Single oocyte (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_Oo01_12_S6_IL10

description:
DRaqL - Protease - Smart-seq2
FF24h_Oo01_12_S6_IL10

value: Secondary-antral


title: SI_P5

value: Nmur1+ Eosinophils


title: SI_P8


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL07

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL07


title: EX8V-4

description: Somatic Cell Contamination in Sperm


title: GD7H-7

description: Somatic Cell Contamination in Sperm


title: EX8V-8

description: Somatic Cell Contamination in Sperm


title: HEK293 cells, NONOTFE3mRuby2 (NE), biological rep 1


title: SI_P4


title: EX8V-10

description: Somatic Cell Contamination in Sperm


title: EX8V-6

description: Somatic Cell Contamination in Sperm


title: GD7H-5

description: Somatic Cell Contamination in Sperm


title: SI_N2


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL06

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL06

value: Neighboring


title: HEK293 cells, SFPQTFE3mRuby2 (SE), biological rep 1


title: SI_3

value: Total eosinophils

value: Wildtype


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL05

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL05


title: EX8V-1

description: Somatic Cell Contamination in Sperm


title: tissue_b


title: SI_P3

value: Small Intestine


title: EX8V-3

description: Somatic Cell Contamination in Sperm


title: EX8V-2

description: Somatic Cell Contamination in Sperm


title: SI_2


title: Colon_4

source_name: Colon

value: Colon


title: SI_P1

value: NMUR1-TdT reporter


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL02

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL02


title: HEK293 cells, PRCCTFE3mRuby2 (PE), biological rep 2


title: EX8V-7

description: Somatic Cell Contamination in Sperm


title: EX8V-5

description: Somatic Cell Contamination in Sperm


title: SI_N7

value: Nmur1- Eosinophils

value: 8-12 weeks


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL01

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL01


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL04

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL04


title: HEK293 cells, TFE3mRuby2 (E), biological rep 1


title: Lung_3

source_name: Lung

value: Lung

value: pooled male and female


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL12

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL12

value: LCM (24 h Formalin-fixed)

value: Non-neighboring


title: Skin_1

source_name: Skin

value: Skin


title: HEK293 cells, SFPQTFE3mRuby2 (SE), biological rep 2


title: HEK293 cells, PRCCTFE3mRuby2 (PE), biological rep 1


title: Colon_2


title: SP_3

value: Spleen


title: HEK293 cells, NONOmRuby2 (N), biological rep 2

value: Immortalized human embryonic kidney cells


title: SP_4


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC13_24_S5_IL03

description:
DRaqL - Protease - Smart-seq2
FF24h_GC13_24_S5_IL03

value: gene expression


title: SP_2


title: SP_1


title: HEK293 cells, NONOmRuby2 (N), biological rep 1


title: Colon_1


title: HEK293 cells, TFE3mRuby2 (E), biological rep 2


title: SI_1


title: Skin_4


title: Skin_2


title: HEK293 cells, PRCCmRuby2 (P), biological rep 2


title: Lung_1


title: Blood_3

source_name: Blood

value: Blood


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL11

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL11


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL10

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL10


title: HEK293 cells, PRCCmRuby2 (P), biological rep 1


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL09

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL09


title: Blood_4


title: HEK293 cells, mRuby (Rb), biological rep 2

value: mRuby control


title: Blood_2

value: Total eosinophils


title: HEK293 cells, SFPQmRuby2 (S), biological rep 2

value: SFPQmRuby


title: BM_2

source_name: Bone Marrow

value: Bone Marrow

value: Wildtype


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL08

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL08


title: BM_3

description:
bulk RNA-seq
full-length gene expression
Smart-seq2


title: HEK293 cells, mRuby (Rb), biological rep 1


title: HEK293 cells, SFPQmRuby2 (S), biological rep 1


title: Blood_1


title: SI_4

value: Small Intestine


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL07

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL07


title: BM_1


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL06

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL06

value: Neighboring


title: Lung_2

value: 8-12 weeks


title: cuttag, Rxrg, KO, 2

description:
CUT&Tag to identify DNA binding sites
DNA-seq

data_processing:
For RNA-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3.
For ATAC-seq/CUTTag-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome and advanced filtering of bad-quality, blacklist reads and duplicates were done using bowtie2(v2.2.5), samtools(v1.10), bedtools(v2.29.2) and picard(v2.23.8).
Assembly: mm10
Supplementary files format and content: TPM expression matrix files were extracted from RSEM gene-results and initially filtered for expressed protein-coding genes.
Supplementary files format and content: bigwig files contain genome-wide signal which were generated from clean bam files using deeptools(v3.5.0) 'bamCoverage -e250 -bs100 --normalizedUsing RPKM'.
Library strategy: CUT&Tag-seq

growth_protocol:
primary small intestine ILC2s or small intestinal ILC2s were cultured in vitro with IL-2 and IL-7, or IL-2, IL-7 and IL-25, for 4, 48 and 72 hours
small intestinal ILC2s were cultured with IL-2 and IL-7, or IL-2, IL-7 and IL-25, for 4, 48 and 72 hours

extract_protocol:
DNA and RNA were extracted from cells using AMPure XP beads (Backman)
Full-length Smart-seq2, ATAC-seq and CUT&Tag-seq
RNA-seq and DNA-seq

treatment_protocol: The mice were at the steady state or treated with IL-25 or PBS for 2 days

value: KO

value: primary small intestine ILC2s

value: steady state

tag: treatment time

tag: antibody

value: Anti-RXRγ antibody (Abcam, Cat# ab15518); Goat Anti-Rabbit IgG Antibody (H&L) [HRP], pAb (Genscript, Cat# A00098)


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL05

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL05

value: LCM (24 h Formalin-fixed)


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL04

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL04


title: SNU449_AxlKO_plusRego_r3

city: Vienna

first: Wolfgang

last: Mikulits

address: Borschkegasse 8A

country: Austria

institute: Medical University of Vienna

description:
Axl_Rego_Quantseq_star253a_GRCh38v40.SS2_DESeq2-220726_AxlKO.minusRego_VS_AxlKO.plusRego_Prep.Date_DEtable.txt
Axl_Rego_Quantseq_star253a_GRCh38v40.SS2_DESeq2-220726_minusRego_VS_plusRego_Prep.Date_DEtable.txt

data_processing:
Computational trimming of poly-As from the 3’-ends of the 100 bp long reads was performed with cutadapt (v. 4.0; with options -O 3 -e 0.05 -m 20 --max-n 2), retaining reads with a trimmed length of at least 20 nt.
Reads were aligned to the human genome GRCh38.v40 and the spike-in sequences (Lexogen “SIRV-Set3”) by STAR 2.5.3a (27), with up to 1000 hits, a maximum error rate of 5%, and counts per gene as output.
These count tables were generated on the basis of the GENCODE annotation v40 concatenated with the SIRV and ERCC annotation.
Assembly: human genome GRCh38.v40
Supplementary files format and content: contain information about: "gene_id" "baseMean" "log2FoldChange" "lfcSE" "stat" "pvalue" "padj" "absLog2FC" "SNU449_AxlKO_parental_r1" "SNU449_AxlKO_parental_r2" "SNU449_AxlKO_parental_r3" "SNU449_AxlKO_plusRego_r1" "SNU449_AxlKO_plusRego_r2" "SNU449_AxlKO_plusRego_r3" "AxlKO.minusRego.AVG" "AxlKO.plusRego.AVG" "chrom_name" "source" "type" "start" "end" "score" "strand"

growth_protocol: SNU449 and derived HCC cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. SNU449 and derived HCC cells were additionally treated with Regorafenib every time after splitting.

extract_protocol:
Total RNA was isolated using the Monarch total RNA miniprep kit (New England Biolabs, Ipswich, Massachusetts, USA).
Library preparation and sequencing was performed by Lexogen (Greenland, New Hampshire, USA). In brief, quality controlled and quantified RNA was used to prepare a QuantSeq 3’ mRNA-seq (fwd) library suitable for Illumina sequencing (12 cycles of library amplification, paired-end 100 nt sequencing).

treatment_protocol: To generate resistant cell lines, SNU449 and SNU449-Axl-KO were initially treated with 50% of the IC50 concentration of Rego (TargetMol Chemicals, Boston, USA). The concentrations was increased by 50% of the IC50 every two weeks until 2 x IC50 was reached and cells proliferated under high concentrations

value: liver

value: Hepatocellular carcinoma cell line

value: Axl KO

value: Regorafenib long-term


title: cuttag, Rxrg, WT, 2

value: pooled male and female

value: WT


title: cuttag, Rxrg, WT, 1


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL03

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL03

value: gene expression


title: cuttag, H3K27me3, KO

value: Anti-Histone H3 (trimethyl K27) antibody (Abcam, Cat# ab6002); Goat anti-mouse IgG (H+L) (Jackson ImmunoResearch, Cat# 115-005-003)


title: cuttag, H3K27me3, WT


title: cuttag, Rxrg, KO, 1


title: SNU449_AxlKO_plusRego_r1


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL02

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL02


title: Single granulosa cell (DRaqL - Protease - Smart-seq2) Formalin-fixed(24h)_GC01_12_S4_IL01

description:
DRaqL - Protease - Smart-seq2
FF24h_GC01_12_S4_IL01


title: cuttag, H3K27ac, WT, 1

value: Acetyl-Histone H3 (Lys27) Antibody (Cell Signaling Technology, Cat# 4353S); Goat Anti-Rabbit IgG Antibody (H&L) [HRP], pAb (Genscript, Cat# A00098)


title: SNU449_AxlKO_parental_r3

description:
Axl_Rego_Quantseq_star253a_GRCh38v40.SS2_DESeq2-220726_AxlKO.minusRego_VS_AxlWT.plusRego_Prep.Date_DEtable.txt
Axl_Rego_Quantseq_star253a_GRCh38v40.SS2_DESeq2-220726_AxlWT_VS_AxlKO_Prep.Date_DEtable.txt

value: naive


title: ATAC, KO, 2

description:
Assay for Transposase-Accessible Chromatin
DNA-seq

data_processing:
For RNA-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3.
For ATAC-seq/CUTTag-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome and advanced filtering of bad-quality, blacklist reads and duplicates were done using bowtie2(v2.2.5), samtools(v1.10), bedtools(v2.29.2) and picard(v2.23.8).
Assembly: mm10
Supplementary files format and content: TPM expression matrix files were extracted from RSEM gene-results and initially filtered for expressed protein-coding genes.
Supplementary files format and content: bigwig files contain genome-wide signal which were generated from clean bam files using deeptools(v3.5.0) 'bamCoverage -e250 -bs100 --normalizedUsing RPKM'.

value: Small Intestine


title: cuttag, H3K27ac, WT, 2

value: 8-12 weeks


title: SNU449_AxlKO_parental_r2


title: Single oocyte (DRaqL - SMART-Seq v4 3' DE Kit) DpOo01_10_S7_IL10

description:
DRaqL - SMART-Seq v4 3' DE Kit
IL10_DpOo01_10_S7

extract_protocol:
A Smart-seq v4 3’ DE Kit (Takara Bio) was adapted to DRaqL as follows.  Cells were isolated with LCM in 6.4 μL of cell lysis buffer (0.25 μL of 40 U/μL Takara RNase Inhibitor, 0.4 μL of 100 mM DTT, 0.16 μL of 1:500,000 diluted ERCC RNA Spike-In Mix 1, 0.4 μL of 5% SDc, and 5.19 μL of nuclease-free water) in the caps of PCR tubes, and spun down into the tubes by brief centrifugation.  Cells were then lysed at 72°C for 3 min, followed by the addition of 2.8 μL quenching buffer (0.7 μL of Triton X-100, 0.7 μL of 2% BSA, and 1.4 μL of 5× SuperScript II buffer [Thermo Fisher]) to reduce the denaturing effect of SDc.  Then, 2.8 μL of RT oligo (1 μL of 12 μM Oligo dT In-line Primer and 1.8 uL of nuclease-free water: kit components) was added, followed by incubation at 72°C for 90 sec.  Reverse transcription was performed by adding 7.5 μL of Master Mix (4 ?L of 5× Ultra Low First-Strand Buffer, 1 μL of 48 μM SMART-Seq V4 oligonucleotide, 0.5 μL of 40 U/μL RNase Inhibitor, and 2 μL of SMARTScribe Reverse Transcriptase: kit component) supplemented with 0.25 μL of SuperScript II and 0.25 μL of SuperScript III, and by incubating at 42°C for 90 min and 70°C for 10 min.  Then, cDNA amplification was performed by adding 30 μL of kit component PCR Mix (25 μL of 2× SeqAmp PCR Buffer, 1 μL of 12 μM Blocked PCR Primer II A, 1 μL of SeqAmp DNA polymerase, and 3μL of nuclease-free water) and applying the thermal cycling program for SMART-seq v4.  The amplified cDNA (50 μL) was purified with a 0.8× volume of AxyPrep MAG PCR clean-up reagent according to the manufacturer’s instructions.
The cDNA synthesis and amplification onward were performed as described previously with minor modifications [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. In brief, the first-strand cDNA was synthesized by SuperScript III [Thermo Fisher] and incubating at 50℃  for 5 min followed by heat inactivation at 70℃  for 10 min.  The excess RT primers were degraded by exonuclease I and incubating at 37℃ for 30 min followed by heat inactivation at 80℃ for 25 min. The first-strand cDNA product was poly dA-tailed by TdT and incubating at 37℃  for 1 min followed by heat inactivation at 70℃ for 10 min. Second-strand cDNA synthesis were performed by adding 9.5 μL reaction mixture of ExTaq, Hot Start version [Takara Bio] and V3[dT]24 primer in the ExTaq buffer with the following thermal cycling program (95℃  for 3 min, 50℃  for 2 min, and 72℃  for 3 min). cDNA amplification was performed by addingthe mixture of V1[dT]24 and ExTaq, Hot Start version [Takara Bio] in the ExTaq buffer with the following thermal cycling program (95℃  for 1 min; 20 cycles of 95℃  for 30 sec, 67℃  for 1 min and 72℃  for 3 min with a 6 sec elongation per cycle; and 72℃  for 10 min).  The amplified cDNA was purified with a 0.6× volume of AxyPrep MAG PCR clean-up reagent (Axygen) according to the manufacturer's instructions. Preparation of the libraries for SC3-seq was performed essentially as previously described (Nakamura et al., 2015)(Nakamura et al., 2017).  For Y-adapter sequencing, single-cell cDNAs were pre-amplified using the primers (V3[dT]24, V1[dT]24) and ExTaq HS with the thermal cycling program (95℃  for 3 min; 4 cycles of 95°C for 30 sec, 67℃  for 1 min and 72℃  for 5 min; 72℃  for 10 min). Pre-amplified cDNAs were then subjected to the primer-dimer removal, sonication, end polishing, and the size selection as in SC3-seq. Then, purified cDNA was dA-tailed in a 10 μL dA tailing mixture with incubation at 72℃  for 10 min. The dA-tailed product was subjected to the Y-shaped adaptor ligation by adding a mixture of Y-adaptor and NEB Next Quick Ligation Reaction Buffer and incubating at 20℃  for 15 min and at 72℃  for 20 min. The ligation product was purified with a 0.9×volume of AxyPrep reagent, and subjected to additional PCR amplification in 20 μL with the thermal cycling program (95℃  for 3 min, 55℃  for 1 min, and 72℃  for 1 min; 11 cycles of 95℃  for 30 sec, 60℃  for 1 min, and 72℃  for 1 min; and 72℃  for 3 min), followed by DNA purification with a 0.9×volume of AxyPrep reagent.

value: LCM

value: Secondary-antral


title: ATAC, WT, 1

value: primary small intestine ILC2s

value: steady state


title: ATAC, WT, 2


title: iILC2, KO, 3

description:
full-length gene expression
Smart-seq2
iKO_3
SS2.nILC2_iILC2.Ctrl_cKO.tpm_matrix.csv

value: KO


title: SNU449_AxlKO_parental_r1

value: liver