title: WT rep2

extract_protocol:
Mice were euthanized by CO2 inhalation and lungs were immediately perfused with 20 mL ice-cold PBS. Lungs were cut in small pieces with scissors, enzymatically digested at 37°C for 45 minutes with a solution containing collagenase IV (1mg/ml), hyaluronidase (0.1mg/ml) and DNase (4.5mg/ml) (Sigma-Aldrich). Cells were then collected, filtered and red blood cells were lysed at RT for 5 minutes with ACK Lysing Buffer (Lonza). Cells were then collected, filtered and pooled as follows: 3 untreated-chimera, 3 silibinin-treated, 3 baricitinib-treated and 3 vFLIP-tg mice. The cells were washed with PBS 1x, re-suspended in RPMI 1640 medium supplemented with 5% bovine serum albumin and counted. Cell viability was determined by Trypan blue exclusion. For each sample, cells were resuspended in RPMI supplemented with 5% FBS to a final concentration of 106 /ml for single cell analysis. Cell suspension were processed using the 10x Genomics Chromium Controller and the Chromium NextGEM Single Cell 3′ GEM, Library& Gel Bead kit v3.1 (Pleasanton, California, United States) following the stand-ard manufacturer’s instructions. In brief, 10,000 live cells were loaded onto the Chromium controller to recover 4,000 single cell GEMs per inlet uniquely barcoded. After synthesis of cDNA, sequencing libraries were generated. Final 10X library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies, Santa Clara, CA, USA) and then sequenced on the Illu-mina NextSeq500 (Illumina, San Diego CA, USA).
After synthesis of cDNA, sequencing libraries were generated. Final 10X library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies, Santa Clara, CA, USA) and then sequenced on the Illu-mina NextSeq500 (Illumina, San Diego CA, USA).

value: WT


title: AAVS1_REP1

status: Public on Sep 09 2021

type: SRA

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

country: USA

institute: Dana Faber Cancer Institute

description: CAL-120 knocked out with AAVS1

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina Bcl2fastq v2.18
Reads were aligned to mm10 using STAR
For fpkm calculation cufflinks was used.
Genome_build: hg19
Supplementary_files_format_and_content: csv file of FPKM table

molecule: polyA RNA

organism: Homo sapiens

source_name: breast cancer cells

growth_protocol: CAL-120 cells were cultured in DMEM plus 10% FBS

extract_protocol:
RNA was extracted from cells with the RNeasy Mini Kit (Qiagen).
The Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 500 ng of purified total RNA, using RNA sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit (NEB #E7760).  according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; pooled uniquely indexed RNA-seq libraries in equimolar ratios, and sequenced these to a target depth of 40M reads on an Illumina NextSeq500 run with single-end 75bp reads.

treatment_protocol: CAL-120 cells were treated with DMSO or  300nM infigratinib, gene knockouts

tag: cell line

tag: treatment

value: knocked out with AAVS1


title: WT rep1

city: Verona

first: Stefano

last: Ugel

address: Piazzale L.A. Scuro, 10

department: Medicine

country: Italy

institute: University and Hospital Trust of Verona

data_processing:
Alignment, barcode processing and UMI counting for each sample was performed using 10x Cell Ranger software v.3.1.0 (cellranger count pipeline) with parameter --expect-cells=4000
Genome_build: mm10
Supplementary_files_format_and_content: Feature-barcode matrix for each sample in the format returned by 10x cellranger count pipeline

organism: Mus musculus

source_name: Lung immune cells

tag: strain

tag: tissue

value: Lung

tag: cell type

value: Lung immune cells


title: M1_Skin_S13

city: Rochester

first: Yang

last: Zhao

state: NY

address: 60 Crittenden Blvd, Apt1240

department: Biology

institute: University of Rochester

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
cleaned reads were mapped to the genome by  STAR_2.5.2b
gene expression (TPM and reads counts) were calculated by salmon 1.4.0
regions of differential methylation were called by edgeR package in 100 window resolution (R version 3.3.2)
Genome_build: Mouse (Mus musculus): mm10
Genome_build: Blind mole rat (Spalax ehrenbergi):GCF_000622305.1_S.galili_v1.0

molecule: total RNA

source_name: Skin

growth_protocol: Fibroblasts were maintained at 37 °C incubator in an atmosphere of 5% CO2 and 3% O2 on treated polystyrene culture dishes (Corning) in EMEM media (ATCC) with 15% (vol/vol) fetal bovine serum (FBS).

extract_protocol:
For RNAseq, was extracted using a Quick-RNA MiniPrep Kit (Zymo), with a DNase I on column digestion to remove genomic DNA contamination; For MeDIP, genomic DNA was extracted using a Zymo Quick-DNA Miniprep Plus Kit.
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.

treatment_protocol: No treatment

value: Wild-caught

value: Skin


title: M1_Spleen_S18

source_name: Spleen

value: Spleen


title: sgAR;SPOPmut_DHT_rep.4

city: New York

first: Ivana

last: Grbesa

address: 413 E 69th St

department: Urology

institute: Weill Cornell Medicine

data_processing:
Reads were aligned to mouse genome  with Bowtie2 v.2.3.4.1.
Genome_build: mm10 genome

source_name: prostate organoids

growth_protocol: Murine organoids were grown in mouse organoid media as per standard protocol.

extract_protocol:
Total RNA was extracted, and DNaseI treated by Maxwell 16 LEV simplyRNA Cells Kit (Promega, Cat# AS1270) and Maxwell nucleic-acid extraction instrument (Promega). Nanodrop quantified RNA was checked by Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies). Samples with RNA integrity number > 10 were used for library preparation.
TruSeq Stranded mRNA  Library Preparation (Poly-  A selection and Stranded  RNA-Seq)

treatment_protocol: Control organoids (with sgNT or sgAR)  were treated for 24h with 10 nM DHT  in mouse organoid media without mEGF.

value: prostate

value: 10 nM DHT

tag: genotype/variation

value: with sgAR (targeting AR exon 2 of NM_013476.4)


title: anti-GFP-YFP-PIF3-Dark-Rep1

city: Paris

first: Clara

last: Bourbousse

address: 9 quai Saint Bernard

department: UMR 7622 LBD

country: France

institute: Sorbonne Université

description: ChIP DNA

library_source: genomic

data_processing:
trimming using trim_galore with options “--phred33 --paired -q 20 --stringency 1 --length 35”
mapping to the TAIR10 genome using bowtie2 with options “--very-sensitive -I 150 -X 2000 -p 20 --no-mixed”.
filtering using samtools  with options “view -hb -F 1804 –L selected_TAIR10_genome_Chr.bed”, which corresponds to the TAIR10 genome after filtering out genomic regions with aberrant coverage or low sequence complexity (retrieved from Quadrana et al. eLife (2016))
Browser tracks were generated using deeptools function bamCoverage with options “--binSize 20 --normalizeUsingRPKM --extendReads --centerReads --ignoreForNormalization ChrC ChrM”.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 5-day-old Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were sterilized with a solution of 75% sodium hypochlorite and 0.1% Tween-20 and stratified at 4°C during 3 days in darkness.  Seedlings were grown in Murashige and Skoog (MS) medium.

extract_protocol:
ChIP experiments were performed as in Fiorucci, Bourbousse et al., Genome Biology (2019)
NEBNext Ultra II DNA Library Prep Kit was used, PE 150bp reads were produced

treatment_protocol: Light: white light (100 umol m-2 s-1) in a 16-h light/8-h dark period. Dark: continuous darkness.

tag: genotype

value: dark

tag: agent

tag: antibody

value: anti-GFP (Life Technologies #11122)


title: shKHSRP_2_rep2

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

country: China

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
data type:ChIP-seq; data processing: For overall ChIP-seq datasets, reads were aligned to the Homo sapiens genome (Ensembl GRCh38.p5) using Bowtie2 PE mode with default parameters. Only reads with mapping quality score >30 were retained for further analysis by SAMtools. Two biological replicates were merged to create ‘Tag Directory’ file by ‘makeTagDirectory’. Peak finding and downstream data analysis were performed using HOMER software by ‘findPeaks’ with factor mode.
data type:RNA-seq; data processing: RNA-seq reads were aligned to Homo sapiens genome (Ensembl GRCh38.p5) using Tophat2 PE mode with the default parameters, and uniquely mapped reads were retained for further analysis filter by SAMtools. HTSeq-counts were used for calculating gene counts, and then normalized for transcript per million (TPM) using in-house scripts.
data type:eCLIP-seq; data processing: Peaks were called with clipper software for eCLIP-seq.
Genome_build: Ensembl GRCh38.p5
Supplementary_files_format_and_content: peaks bed file for ChIP-seq; expression matix for RNA-seq; peaks bed file for eCLIP-seq

source_name: THP-1 cell line

extract_protocol:
THP-1 cells were treated with QKI5 shRNA (shQKI5-1/shQKI5-2) or shCtrl.
The cells were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody

tag: clip antibody

value: KHSRP knock down


title: sgAR;SPOPmut_DHT_rep.3


title: anti-GFP-WT-Rep2

description: ChIP DNA


title: M2_Liver_S4

source_name: Liver

value: Liver


title: exp020821 P8 rep 1

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description:
phaffi_plus_transgenes_020821.fa.gz
dalvie020821_intCt.txt.gz
dalvie020821_l2cpm.txt.gz

data_processing:
MiSeq sequencing using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
3’ DGE FASTQ sequencing reads were collapsed to one representative per unique molecular identifier using a custom script. Gene expression was quantified using salmon (version 1.3.0, Patro et al., 2017) using the indicated Komagataella transcriptomes plus transgenes as selective alignment targets.  The resulting counts were summarized to the gene level using tximport (version 1.12.3) and counts per million (cpm) were calculated using utilities implement in edgeR (version 3.26.8, Chen et al., 2014). The cpm values with a +1 offset were transformed to log2 space for visualization.
Genome_build: Komagataella phaffi WT (PRJNA304977) with indicated transcriptomes
Supplementary_files_format_and_content: phaffi_plus_transgenes_020821.fa.gz is a fasta transcriptome file used for the indicated samples
Supplementary_files_format_and_content: phaffi_plus_transgenes_031020.fa.gz is a fasta transcriptome file used for the indicated samples
Supplementary_files_format_and_content: dalvie020821_intCt.txt.gz is tab delimited integer count data prepared using the phaffi_plus_transgenes_020821.fa.gz target
Supplementary_files_format_and_content: dalvie020821_l2cpm.txt.gz is tab delimited counts per million with a plus 1 offset prepared using the phaffi_plus_transgenes_020821.fa.gz target
Supplementary_files_format_and_content: dalvie031020_intCt.txt.gz is tab delimited integer count data prepared using the phaffi_plus_transgenes_031020.fa.gz target
Supplementary_files_format_and_content: dalvie031020_l2cpm.txt.gz is tab delimited counts per million with a plus 1 offset prepared using the phaffi_plus_transgenes_031020.fa.gz target

organism: Komagataella phaffii

source_name: bulk yeast cell culture

growth_protocol: Cell were harvested after 18 h of production at 3 mL plate scale. Cells were cultivated in complex media (potassium phosphate buffer pH 6.5, 1.34% nitrogen base w/o amino acids, 1% yeast extract, 2% peptone).

extract_protocol:
RNA was extracted and purified according to the Qiagen RNeasy kit (cat #74104) and RNA quality was analyzed to ensure RNA Quality Number >6.5.
3'DGE Nextera

treatment_protocol: Cells were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and resuspended in fresh media with 3% methanol to induce recombinant gene expression.

tag: transgene

value: P8 control


title: BRG_KO1_REP1

description: CAL-120 knocked out with BRG1

value: knocked out with BRG1


title: M1_Muscle_S28

source_name: Muscle

value: Muscle


title: M1_Liver_S3


title: sgAR;SPOPmut_DHT_rep.2


title: shKHSRP_2_rep1


title: anti-HY5-det1-Rep2

description: ChIP DNA

value: light

value: 1percent sucrose

value: anti-HY5 (Agrisera AS12 1867)


title: M1_Lung_S23

source_name: Lung

value: Lung


title: shKHSRP_1_rep2


title: sgAR;SPOPmut_DHT_rep.1


title: sgNT;SPOPmut_DHT_rep.4

value: with sgNT (CRISPR control)


title: M1_Kidney_S8

source_name: Kidney

value: Wild-caught

value: Kidney


title: shCtrl2_rep2

value: empty vetor


title: anti-GFP-WT-Rep1

description: ChIP DNA

value: WT


title: anti-HY5-det1-Rep1

description: ChIP DNA


title: sgNT;SPOPmut_DHT_rep.3

value: prostate

value: 10 nM DHT


title: shKHSRP_1_rep1


title: shCtrl2_rep1


title: M1_Intestine_S33

source_name: Intestine

value: Intestine


title: anti-HY5-WT-Rep2

description: ChIP DNA


title: anti-HY5-WT-Rep1

description: ChIP DNA


title: KO_female [LM191]

city: Pittsburgh

first: Satdarshan

last: Monga

state: PA

address: S-422 SBST, 200 Lothrop Street

department: Pathology

institute: University of Pittsburgh School of Medicine

data_processing:
Samples were sequenced by llumina Novaseq 6000 with paired-end 150bp reads, with 20 million reads per end per sample, by Novogene Inc. Base-calling was performed by Novogene Inc. with the latest Illumina software. They also trimmed adapters, removed reads containing N > 10%, and removed reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
CLC Genomics Workbench 20.0.3 was used to align reads to the transcriptome (GRCm38), perform log2-transform and TMM normalization, and analyze differential expression using edgeR to calculate TPM values.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values for each gene by sample

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen and stored at -80C. RNA was harvested using Trizol reagent and purified with Qiagen RNeasy Mini Prep kit (Cat.No. 74104). DNA was digested using Qiagen RNase-free DNase Set (Cat.No 79254).
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

tag: strain background

value: Foxa3-Cre YAP1 KO

tag: Sex

value: female


title: sgNT;SPOPmut_DHT_rep.2


title: CLIP_SETD1A_rep1

extract_protocol:
THP-1 cells were UV-crosslinked and lysed then proetin-RNA complexes were isolated with indicated antibodies. Then the RNA was purified for subsquential processes.
Libraries were  prepared as described in "Van Nostrand, E. L. et al. Nat Methods, 2016, 13, 508-514"and sequenced by using Illumina Hiseq 1000 with pair end 150bp read length.

value: SETD1A(ab70378, abcam)


title: KO_female [LM189]

value: Liver


title: sgNT;SPOPmut_DHT_rep.1


title: CLIP_NUDT21_rep1

value: NUDT21(ab183660, abcam)


title: CLIP_SETD1A_rep2


title: sgAR;Control_DHT_rep.3

value: with sgAR (targeting AR exon 2 of NM_013476.4)


title: anti-HY5-hy5-Rep1

description: ChIP DNA

value: light

value: 1percent sucrose


title: CLIP_input_SETD1A_rep2


title: input-WT-Rep2

description: ChIP DNA

value: input


title: CLIP_NUDT21_rep2


title: sgAR;Control_DHT_rep.4


title: KO_female [LM74]


title: KO_male [LM194]

value: male


title: KO_male [LM188]


title: CLIP_input_NUDT21_rep2


title: anti-GFP-35SGFP-Rep2

description: ChIP DNA

value: anti-GFP (Life Technologies #11122)


title: KO_male [LM187]


title: input-WT-Rep1

description: ChIP DNA


title: CLIP_input_NUDT21_rep1


title: sgNT;Control_DHT_rep.3

value: with sgNT (CRISPR control)


title: sgAR;Control_DHT_rep.2


title: CLIP_input_SETD1A_rep1


title: anti-GFP-35SHY5GFP-Rep2

description: ChIP DNA


title: WT_male [LM196B]


title: sgAR;Control_DHT_rep.1


title: WT_female [LM75]


title: anti-GFP-35SHY5GFP-Rep1

description: ChIP DNA


title: WT_male [LM205]


title: anti-HY5-hy5-Rep2

description: ChIP DNA

value: anti-HY5 (Agrisera AS12 1867)


title: anti-GFP-35SGFP-Rep1

description: ChIP DNA


title: WT_female [LM193]

value: WT


title: sgNT;Control_DHT_rep.2

value: prostate


title: CLIP_input_KHSRP_rep2


title: sgNT;Control_DHT_rep.4

description: This sample not included in the final analysis

value: 10 nM DHT


title: input-35SHY5GFP-Rep2

description: ChIP DNA


title: input-35SHY5GFP-Rep1

description: ChIP DNA


title: CLIP_input_ELAVL1_rep2


title: CLIP_input_KHSRP_rep1


title: mWake tdTomato+ cells, scRNA-Seq - Replicate 2 (BB5)

city: Baltimore

first: Mark

last: Wu

address: 855 N. Wolfe Street

institute: Johns Hopkins University

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Barcodes, features, matrix files.
mWake_Neurons_matrix.rds (count matrix of aggregated dataset)
mWake_Neurons.rds (umap data (2d) of aggregated dataset)

source_name: mWake tdTomato+ cells

extract_protocol: scRNA-Seq following 10x V3.0 guideline

value: Hypothalamus

value: mWake tdTomato+ cells

tag: age

value: 7 weeks old

value: Male


title: WT_female [LM192]

value: female

value: Liver


title: Rat- Brain -Mock Rep2

city: Jerusalem

first: Sebastian

last: Kadener

address: SIlberman Institute of Life Sciences, Edmund J. Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
alignemnets to the genomes were done with STAR_2.6.1a_08-27
back spliced and linear reads was done using SRCP
Genome_build: hg38
Genome_build: mm10
Genome_build: rheMac10
Genome_build: rn5
Genome_build: dm6
Supplementary_files_format_and_content: Tables with  back-spliced reads and linear spliced reads.

organism: Rattus norvegicus

source_name: Rat Brain Total RNA (R1434035-50) Biochain

extract_protocol:
RNA purchase/extraction:  Human Adult Normal Brain Total RNA (R1234035-50), Human Adult Normal Cerebellum Total RNA (R1234039-50), Rat Brain Total RNA (R1434035-50), Monkey(Rh) Brain (R1534035-50) Total RNA was obtained by BioChain. Human Blood Total RNA (HR-705) was obtained from Zyagen.One C57BL/6 male and one female were sacrificed at p21, different brain regions were harvested (cerebellum, cortex, olfactory bulb, brain stem and, thalamus) by the Nelson’s lab at Brandeis University. The RNA was extracted with TRI reagent (Sigma, Aldrich) , followed by Zymo RNA cleaning and concentrator -25 Kit (Zymo), according to the manufactures’ instruction. We collected and dissected 10 days old D. melanogaster (Canton-S) heads and brains. Total RNA was  extracted with TRI reagent (Sigma, Aldrich), followed by DNase (DnaseI, NEB) treatment.
Recovered RNA was used to prepare a total RNA library, adapting the protocol from Shishkin et al. , Nature 2015. Specifically, we prepared one library for the RNAseR treated samples and one for the Mock ones. Briefly, RNA was fragmented for 3 min at 92°C in FAstAP 2X buffer (ThermoFisher). Subsequently, samples were dephosphorylated with FastAP enzyme (ThermoFisher), the first linker was ligated, and samples belonging to the same library were pulled together. Retro-transcription was performed using Affinity Script (Agilent). After second ligation, we performed PCR to add the external barcode. For Human Blood RNA samples and D. melanogaster samples, libraries were prepared using the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 by PerkinElmer, following the manufacturer’s instructions.
RnaseR vs Mock ribodepleted total RNA library
The samples were sequenced by Novogene Corporation Inc.(8801 Folsom BLVD, Suite 290, Sacramento, CA 95826)- HiSeq 1% PhiX with HiSeq-4000sequencer

treatment_protocol:
ribodepletion:  For mammalian RNA, ribodepletion was performed on 5ug of Total RNA with Ribo-Zero Gold rRNA Removal Kit according to the manufacturer’s instruction. Degradation of rRNA was checked by TapeStation. For Drosophila RNA, ribodepletion was performed with an homemade protocol. Briefly, rRNA was hybridized with specific DNA probes and degraded with RNasH , followed by DNase treatment for removing the DNA probes from the sample.
RNaseR:  From the collected ribodepleted RNA, 2/5 of the volume was treated with 6Units of RNAseR (Lucigen) or with buffer only (Mock) for 15 min at 37°C. The RNA was immediately extracted with TRI reagent (Sigma, Aldrich) according to the manufacture’s instruction.

value: 8-20 weeks

tag: treatments

value: ribodepletion, mock


title: CLIP_input_ADAR_rep2


title: mWake tdTomato+ cells, scRNA-Seq - Replicate 1 (BB4)


title: mWake tdTomato+ cells, scRNA-Seq - Replicate 3 (BB6)


title: Rat-Brain-Mock

description: Male, 8-20 weeks

data_processing:
Alignments to the genomes were done with STAR_2.6.1a_08-27.
Back spliced and linear reads was done using SRCP.
Genome_build: Human hg38 (GRCh38)
Genome_build: Mouse mm10 (GRCm38)
Genome_build: Rhesus rheMac10 (Mmul_10)
Genome_build: Rat rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *.txt: Tables with back-spliced reads and linear spliced reads.

extract_protocol:
RNA purchase/extraction: Human Adult Normal Brain Total RNA (R1234035-50), Human Adult Normal Cerebellum Total RNA (R1234039-50), Rat Brain Total RNA (R1434035-50), Monkey(Rh) Brain (R1534035-50) Total RNA was obtained by BioChain. Human Blood Total RNA (HR-705) was obtained from Zyagen. One C57BL/6 male and one female mouse were sacrificed at p21, different brain regions were harvested (cerebellum, cortex, olfactory bulb, brain stem and thalamus) by the Nelson’s lab at Brandeis University. The RNA was extracted with TRI reagent (Sigma, Aldrich), followed by Zymo RNA cleaning and concentrator -25 Kit (Zymo), according to the manufacturers’ instruction.
Recovered RNA was used to prepare a total RNA library, adapting the protocol from Shishkin et al., Nature 2015. Specifically, we prepared one library for the RNaseR treated samples and one for the Mock ones. Briefly, RNA was fragmented for 3 min at 92°C in FAstAP 2X buffer (ThermoFisher). Subsequently, samples were dephosphorylated with FastAP enzyme (ThermoFisher), the first linker was ligated, and samples belonging to the same library were pulled together. Retro-transcription was performed using Affinity Script (Agilent). After second ligation, we performed PCR to add the external barcode.
RNaseR vs. Mock ribodepleted total RNA library.
The samples were sequenced by Novogene Corporation Inc. (8801 Folsom BLVD, Suite 290, Sacramento, CA 95826) - HiSeq 1% PhiX.

treatment_protocol:
Ribodepletion: Ribodepletion was performed on 5ug of Total RNA with Ribo-Zero Gold rRNA Removal Kit according to the manufacturer’s instruction. Degradation of rRNA was checked by TapeStation.
RNaseR: From the collected ribodepleted RNA, 2/5 of the volume was treated with 6 Units of RNAseR (Lucigen) or with buffer only (Mock) for 15 min at 37°C. The RNA was immediately extracted with TRI reagent (Sigma, Aldrich) according to the manufacturer's instruction.

value: Brain

value: Ribodepletion, mock


title: aGVHD_V

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
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
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited tex files include FPKM values for each samples

source_name: Bone marrow niche cells

growth_protocol: Cells were directly isolated from mice.

extract_protocol:
We isolated stromal cells from mice by fluorescence activated cell sorting (FACS) after labeling CD45, lineage mix, and CD71 to deplete hematopoietic cells, and Calcein AM and DAPI to eliminate the dead cells
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: 5x106 BM nucleated cells (BMNCs) from B6.SJL mice (CD45.1+) were intravenously injected into female CB6F1 recipients (CD45.2+) 4 hours after sub-lethal- irradiation (4.0 Gy, twice) to establish the BMT model. Additional spleen cells (6x107) from female C57BL/6 mice were injected into the BMT mice to establish the aGVHD model.

value: Bone marrow niche cells

value: bone marrow transplantation and splenic cell infusion (to develop aGVHD)


title: Rat-Brain-RNaseR

description: Male, 8-20 weeks

value: Ribodepletion, RNaseR


title: CLIP_input_ADAR_rep1


title: WT_male [LM186]

value: male


title: BMT

value: bone marrow transplantation


title: CLIP_input_ELAVL1_rep1


title: S2M27: striatum_olanzapine_male 27

status: Public on Sep 08 2021

type: RNA

city: Barcelona

first: Natalia

last: Rodriguez

state: Barcelona

address: Casanova 143

department: Basic Clinical Practice

country: Spain

institute: University of Barcelona

description: gene expression data from striatum dissected from male mice treated with olanzapine 3.5 mg/kg for 28 days

data_processing: RMA processing algorithm (Affymetrix GeneChip Expression Console v1.4 Software). Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)

label: biotin

source_name: striatum, olanzapine

growth_protocol: Mice were maintained at 22ºC on a 12-hour alternating light/dark cycle with ad libitum access to food and water, using a standard chow diet.

extract_protocol: Total RNA was isolated using Trizol reagent and was further purified using the miTotal RNA Extraction Miniprep System (Viogene Biotek Corp).

treatment_protocol: Mice were chronically treated for 28 days with a daily subcutaneous dose of vehicle (saline containing 5% dimethylsulfoxide (DMSO) and 5% Tween 20), risperidone (1 mg/kg) or olanzapine (3.5 mg/kg).

value: striatum

tag: condition

value: olanzapine 3.5 mg/kg

tag: gender


title: sgNT;Control_DHT_rep.1

value: prostate

tag: treatment

value: 10 nM DHT

value: with sgNT (CRISPR control)


title: S2M26: striatum_olanzapine_male 26

hyb_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)


title: S2F25: striatum_olanzapine_female 25

description: gene expression data from striatum dissected from female mice treated with olanzapine 3.5 mg/kg for 28 days

scan_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)


title: S2F7: striatum_olanzapine_female 7

label_protocol: Protocol from Kompetenzzentrum für Fluorescente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany)


title: S1M5: striatum_risperidone_male 5

description: gene expression data from striatum dissected from male mice treated with risperidone 1 mg/kg for 28 days

source_name: striatum, risperidone

value: risperidone 1 mg/kg


title: S2F9: striatum_olanzapine_female 9

value: female


title: S1F4: striatum_risperidone_female 4

description: gene expression data from striatum dissected from female mice treated with risperidone 1 mg/kg for 28 days


title: S2M25: striatum_olanzapine_male 25


title: S1F23: striatum_risperidone_female 23


title: S1M23: striatum_risperidone_male 23


title: SCM19: striatum_control_male 19

description: gene expression data from striatum dissected from male mice treated with vehicle for 28 days

source_name: striatum, control

value: control (vehicle)


title: S2F26: striatum_olanzapine_female 26


title: S1M4: striatum_risperidone_male 4


title: F2M27: fat_olanzapine_male 27

description: gene expression data from visceral adipose tissue dissected from male mice treated with olanzapine 3.5 mg/kg for 28 days

source_name: fat, olanzapine

value: visceral adipose tissue


title: F2M26: fat_olanzapine_male 26


title: SCF2: striatum_control_female 2

description: gene expression data from striatum dissected from female mice treated with vehicle for 28 days


title: F2M9: fat_olanzapine_male 9


title: S2M9: striatum_olanzapine_male 9


title: SCM1: striatum_control_male 1


title: SCF20: striatum_control_female 20


title: S1F6: striatum_risperidone_female 6


title: SCM3: striatum_control_male 3


title: SCM21: striatum_control_male 21


title: S1F5: striatum_risperidone_female 5


title: F2M25: fat_olanzapine_male 25


title: SCF1: striatum_control_female 1


title: S1M24: striatum_risperidone_male 24


title: SCF21: striatum_control_female 21


title: F2F25: fat_olanzapine_female 25

description: gene expression data from visceral adipose tissue dissected from female mice treated with olanzapine 3.5 mg/kg for 28 days


title: F2F9: fat_olanzapine_female 9


title: F2F26: fat_olanzapine_female 26


title: F1M4: fat_risperidone_male 4

description: gene expression data from visceral adipose tissue dissected from male mice treated with risperidone 1 mg/kg for 28 days

source_name: fat, risperidone


title: F1F6: fat_risperidone_female 6

description: gene expression data from visceral adipose tissue dissected from female mice treated with risperidone 1 mg/kg for 28 days


title: F1F5: fat_risperidone_female 5


title: F1M24: fat_risperidone_male 24


title: FCM21: fat_control_male 21

description: gene expression data from visceral adipose tissue dissected from male mice treated with vehicle for 28 days

source_name: fat, control


title: F2F7: fat_olanzapine_female 7


title: FCF2: fat_control_female 2

description: gene expression data from visceral adipose tissue dissected from female mice treated with vehicle for 28 days


title: FCF1: fat_control_female 1


title: FCM3: fat_control_male 3


title: P2F9: pancreas_olanzapine_female 9

description: gene expression data from pancreas dissected from female mice treated with olanzapine 3.5 mg/kg for 28 days

source_name: pancreas, olanzapine

value: pancreas


title: F1M5: fat_risperidone_male 5


title: AAVS1_REP3

description: CAL-120 knocked out with AAVS1

source_name: breast cancer cells

tag: cell line

value: knocked out with AAVS1


title: P2M27: pancreas_olanzapine_male 27

description: gene expression data from pancreas dissected from male mice treated with olanzapine 3.5 mg/kg for 28 days

tag: tissue


title: F1F23: fat_risperidone_female 23


title: F1F4: fat_risperidone_female 4


title: P1M24: pancreas_risperidone_male 24

description: gene expression data from pancreas dissected from male mice treated with risperidone 1 mg/kg for 28 days

source_name: pancreas, risperidone


title: P2M25: pancreas_olanzapine_male 25


title: P2F7: pancreas_olanzapine_female 7


title: FCF20: fat_control_female 20


title: F1M23: fat_risperidone_male 23


title: P1M5: pancreas_risperidone_male 5


title: P2F25: pancreas_olanzapine_female 25


title: FCM1: fat_control_male 1


title: P2F26: pancreas_olanzapine_female 26


title: P1F5: pancreas_risperidone_female 5

description: gene expression data from pancreas dissected from female mice treated with risperidone 1 mg/kg for 28 days


title: FCM19: fat_control_male 19


title: P2M26: pancreas_olanzapine_male 26


title: P2M9: pancreas_olanzapine_male 9


title: FCF21: fat_control_female 21


title: P1M23: pancreas_risperidone_male 23


title: P1F23: pancreas_risperidone_female 23


title: PCF21: pancreas_control_female 21

description: gene expression data from pancreas dissected from female mice treated with vehicle for 28 days

source_name: pancreas, control


title: P1F6: pancreas_risperidone_female 6


title: P1F4: pancreas_risperidone_female 4


title: PCF2: pancreas_control_female 2


title: PCM21: pancreas_control_male 21

description: gene expression data from pancreas dissected from male mice treated with vehicle for 28 days


title: L2M9: liver_olanzapine_male 9

description: gene expression data from liver dissected from male mice treated with olanzapine 3.5 mg/kg for 28 days

source_name: liver, olanzapine

value: liver


title: L2M25: liver_olanzapine_male 25


title: L2F26: liver_olanzapine_female 26

description: gene expression data from liver dissected from female mice treated with olanzapine 3.5 mg/kg for 28 days


title: PCF20: pancreas_control_female 20


title: PCM1: pancreas_control_male 1


title: L2F25: liver_olanzapine_female 25


title: LCM21: liver_control_male 21

description: gene expression data from liver dissected from male mice treated with vehicle for 28 days

source_name: liver, control


title: L2F9: liver_olanzapine_female 9


title: L1F5: liver_risperidone_female 5

description: gene expression data from liver dissected from female mice treated with risperidone 1 mg/kg for 28 days

source_name: liver, risperidone


title: L1M23: liver_risperidone_male 23

description: gene expression data from liver dissected from male mice treated with risperidone 1 mg/kg for 28 days


title: L1F4: liver_risperidone_female 4


title: PCM3: pancreas_control_male 3


title: LCM19: liver_control_male 19


title: PCF1: pancreas_control_female 1


title: L1M5: liver_risperidone_male 5


title: L1M4: liver_risperidone_male 4


title: L2M26: liver_olanzapine_male 26


title: L2M27: liver_olanzapine_male 27


title: PND18_Adipocyte_snRNAseq

city: Detroit

first: James

middle: G.

last: Granneman

state: mi

address: 6135 Woodward

department: CMMG

institute: Wayne State University

description: 10X genomics v2 scRNA-seq

data_processing:
Bulk-RNAseq libraries were sequenced using Illumina HiSeq 4000 with a single-end read format.  Sequencing reads were aligned to the mouse chromosome (mm10) with STAR (v 2.5.2a), and read counts were quantified with HTSeq-count using the Bluebee platform (https://www.bluebee.com).
Single cell (sc) and nuclei (sn)-RNAseq libraries were sequenced using Nextseq500.  Libraries were demultiplexed then processed using 10X Genomics Cellranger (3.0.2) pipeline.  Ambient RNA was cleaned using SoupX R package, and a corrected gene matrix generated (processed file).
Single nuclei (sn) ATAC-seq libraries were sequenced using Nextseq500. Reads were demultiplexed and further processed with the Cellranger ATAC v1.2 pipeline.  Custom peaks were called using the SnapATAC vignette  (https://github.com/r3fang/SnapATAC) using the commands --nomodel --shift 100 --ext 200 --qval 5e-2.  The custom peaks  were used to create a cell-peak matrix using the Cellranger-ATAC reanalyze pipeline (10X Genomics, v 1.2) on aggregated libraries without depth correction.  For each aggregated library, PND06 (gemwell-1), PND18 (gemwell-2), and PND56 (gemwell-3) (processed file).
Genome_build: mm10
Supplementary_files_format_and_content: Bulk RNA-seq: tab-delimited text files
Supplementary_files_format_and_content: scRNA-seq: Matrix table with gene counts
Supplementary_files_format_and_content: snATAC-seq: Aggregated HDF5 Feature Barcode Matrix Format

source_name: Adipocyte (iWAT)

extract_protocol: 10X Genomics v2 single cell RNA kit

tag: strain

value: inguinal white adipose tissue

tag: developmental age

value: Postnatal day 18

tag: cell type

value: Adipocyte

value: Male


title: L1M24: liver_risperidone_male 24

value: male


title: LCM1: liver_control_male 1


title: PND06_Adipocyte_snRNAseq

description: 10X genomics v2 scRNA-seq

value: Postnatal day 06


title: L1F6: liver_risperidone_female 6


title: L2F7: liver_olanzapine_female 7

value: olanzapine 3.5 mg/kg


title: PND06_PND18_PND56_Adipocyte_aggregated_snATACseq

description: 10X Genomics v1 snATAC-seq

extract_protocol: 10X Genomics v1.0 single cell ATAC kit

value: Postnatal day 06, 18, 56


title: LCF2: liver_control_female 2

description: gene expression data from liver dissected from female mice treated with vehicle for 28 days


title: L1F23: liver_risperidone_female 23


title: PND18_LinNeg_SVC_scRNAseq

description: 10X genomics v2 scRNA-seq

source_name: Lineage negative stromal cells (iWAT)

value: Lineage Negative Stromal Cells


title: PND56_Adipocyte_snRNAseq

description: 10X genomics v2 scRNA-seq

value: Postnatal day 56


title: Setd2SRI/wt male, input

city: Houston

first: Cheryl

middle: L

last: Walker

state: TX

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine

data_processing:
Data was mapped to the mouse genome using bowtie2 2.3.4.3
Signal tracks were computed for uniquely mapped reads using bedtools v2.27.1 and igvtools v2.3.93
Genome_build: UCSC build mm10
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in WIG and TDF format

source_name: Brain

growth_protocol: Littermates were sacrificed after birth in standard housing conditions.

extract_protocol:
Brains were flash frozen in liquid nitrogen, pulverized, crosslinked in PBS with 1 % formaldehyde, and followed by quenching with 125 mM glycine.  Chromatin was sonicated with bioruptor (Diagenode) to 150-300 bp and immunoprecipitated using anti-H3K36me3 antibody (Abcam, ab9050).
DNA libraries were prepared with the QIAseq FX DNA Library Kit (Qiagen) and sequenced using NextSeq 500 Illumina generating ~40 million 76 bp single end reads per samples.
ChIP-Seq (All-enzymatic whole genome and hybrid capture library preparation (Qiagen))

tag: genotype

value: post natal day 0


title: Setd2SRI/wt female 2, ChIP-Seq

value: H3K36me3 (Abcam, ab9050)

value: female


title: PND06_PND18_PND56_LinNeg_SVC_aggregated_snATACseq

description: 10X Genomics v1 snATAC-seq


title: LCF1: liver_control_female 1

value: control (vehicle)


title: LCF21: liver_control_female 21


title: Control male 1 & 2, pooled, input

value: wild type


title: LCF20: liver_control_female 20


title: PND56_LinNeg_SVC_scRNAseq

description: 10X genomics v2 scRNA-seq


title: Setd2SRI/wt male, ChIP-Seq


title: PND06_LinNeg_SVC_scRNAseq

description: 10X genomics v2 scRNA-seq


title: Control female 2, ChIP-Seq


title: Control female 1, ChIP-Seq


title: Control male 2, ChIP-Seq


title: Setd2SRI/wt female 2

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
After trimming samples were aligned to mm10 using HISAT2
Features were quantified using featureCounts and the Gencode gene model
Differential gene expression was inferred after RUVSeq normalization using EdgeR; significance was achieved for fold change exceeding 1.5x and FDR-adjusted q-value<0.0.05
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression as read counts for all samples.

extract_protocol:
Brains were flash frozen in liquid nitrogen, pulverized, and homogenized.  Total RNA was isolated with Trizol (Ambion) and treated with DNase to remove the genomic DNA.  Extracted RNA samples underwent quality control assessment using the RNA tape on Tapestation 4200 (Agilent) and were quantified with Qubit Fluorometer (Thermo Fisher).
RNA libraries were prepared with QIAseq Stranded Total RNA library Kit (Qiagen) using 100 ng input RNA.  Ribosomal RNA was depleted with QIAseq FastSelect HMR kit (Qiagen).  RNA was fragmented, reverse transcribed into cDNA, and ligated with Illumina sequencing adaptors at the 5’ and 3’ ends.  The size selection for libraries was performed using SPRIselect beads (Beckman Coulter) and purity of the libraries was analyzed using the High Sensitivity DNA 1000 tape on the Tapestation 4200 (Agilent) with a size of 300 bps.  The prepared libraries were pooled and sequenced using NextSeq 500 (Illumina); generating ~20 million 2×76 bp paired-end reads per samples.


title: Control male 1, ChIP-Seq


title: Setd2SRI/wt female 1


title: Control female 2


title: LCM3: liver_control_male 3


title: Setd2SRI/wt male

description: S-M


title: Control male 1


title: 3-Control

city: Philadelphia

first: Jesse

last: Lee

address: South Pavilion, Room 8-326

institute: University of Pennsylvania

data_processing:
FastQ files were uploaded to the BaseSpace Suite (Ilumina) after sequencing and aligned to the mus musculus 10 (mm10) genome using the STAR aligner within the RNA-Seq Alignment (version 1.1.0) application.
The maximum allowed mismatches were set to 14 bases as recommended by manufacturer.
Output .bam/.bai files were analyzed by CuffDiff using the Cufflinks Assembly & DE (version 2.1.0) application in the BaseSpace Suite to determine differentially expressed genes (DEGs) between experimental groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Liver

extract_protocol:
Mouse organs were stored in TRIzol (Thermo Fisher) at –80°C until analysis. Samples were thawed on ice and allowed to equilibrate to room temperature before RNA was isolated using the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol.
After the quality of RNA was assessed using a 2100 Bioanalyzer (Agilent), samples were prepared using a QuantSeq 3′ mRNA-Seq library prep kit FWD for Illumina (Lexogen) following the manufacturer’s protocol and analyzed on a NextSeq 500 sequencing system(Illumina).

value: WT

value: PBS


title: 11-Control

value: liver


title: 7-Control


title: Control male 2


title: ACO_rep2

city: Austin

first: Yu Jin

last: Jang

state: Texas

address: 2506 Speedway, NMS 4.246

department: Molecular Biosciences

institute: University of Texas at Austin

description: procesed data file: RNAseq_HTSeq_count_matrix.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm10 genome using bowtie2 for ATAC-seq. STAR was used for mapping reads of RNA-seq.
Peaks of ATAC-seq were called using MACS2 peak caller. HTSeq was used for counting reads in exons for RNA-seq.
Genome_build: mm10
Supplementary_files_format_and_content: For ATAC-seq, tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak. For RNA-seq, one tab-delimited text file contains all RNA-seq data. Gene expression was shown as log2(FPKM+1) values for each genes.

source_name: ACO

growth_protocol: Freshly sorted lineage-labeled cells from Scgb1a1-CreERTM;R26RtdTomato or Sftpc-CreERT2;R26RtdTomato mice were resuspended in basic medium (AdDMEM/F12 (Invitrogen) supplemented with B27, 1mM N-Acetylcysteine, 10 mM Nicotinamide). Then, cells were mixed with growth factor-reduced Matrigel at a ratio of 1:1. A 100μl mixture was placed in a 24-well Transwell insert with a 0.4-μm pore. Approximately 10×104 epithelial cells were seeded in each insert. After Matrigel formed a gel, 500μl of culture medium (basic medium supplemented with the growth factors: 50 ng/ml murine EGF, 100 ng/ml human FGF7/KGF, 100 ng/ml human FGF10, 50% WNT3A-conditioned media, 10% RSPO1-conditioned media, 100 ng/ml Noggin) was placed in the lower chamber. Medium was changed every other day and ROCK inhibitor Y27632 (10μM) was added in the medium for the first 2 days of culture. For passages, organoids were removed from the Matrigel by incubation with dispase (1mg/ml) for 40 mins at 37°C, followed by dissociation into single cells using trypLE treatment for 5 min at 37°C. 5~10×10^4 cells were transferred to fresh Matrigel in 24-well Transwell insert.

extract_protocol:
Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) was performed in secretory cells and alveolar type 2 cells isolated from Scgb1a1-CreTM;R26RfGFP;Sftpc-dsRedIRES-DTR mice. Briefly, tagmentation reaction was performed with 50ng of target DNA, and then bPCR-compatible sites and barcode were added into the target DNA by PCR. After cleaning up the PCR products using Zymo DNA clean and concentrator-5 kit, the final product was sequenced using Illumina HiSeq 400 machine.  Global gene expression profiles using RNA-seq were performed in feeder-free cultured organoids derived from secretory cells and alveolar type 2 cells.  Briefly, total RNAs were isolated using the RNeasy plus minikit (Qiagen). mRNAs were enriched from total RNAs, fragmented, and primed. First strand cDNAs were synthesized following by second strand synthesis. The ends of purified double strand cDNAs were repaired, ligated with a barcoded adaptor, and amplified with PCR. Purified final PCR product was sequenced using Illumina NextSeq 500 machine.
ATAC-seq library was constructed using Nextera DNA library prep kit following the manufacturer’s protocol. RNA-seq library was constructed using NEBNext Ultra RNA Library prep kit (NEB, E7530S) according to manufacturer’s instruction.

treatment_protocol: DAPT (20μM) were treated every other day for 14 days.

value: lung

value: alveolar type 2 cell organoids

value: untreated


title: SCO_-D_rep2

value: secretory cell organoids


title: SCO_+D_rep1

value: treated with DAPT


title: 9-Treatment


title: SCO_-D_rep1


title: Setd2SRI/wt female 1, ChIP-Seq


title: scRNA-seq: COL20_ROW34

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

data_processing:
Quality checking of sequence reads was performed by Trim Galore and FastQC/multiQ.
Quantification of mapped sequence reads was calculated by featureCounts.
Genome_build: Mapping was performed by HISAT2 against GRCm38.
Supplementary_files_format_and_content: read count table

source_name: Alveolar type 1 cell

extract_protocol:
The single cell suspension was loaded onto a C1 mRNA Seq HT IFC (Fluidigm, South San Francisco, CA), designed to capture 800 single cells between diameters of 10-17 um. The IFC was run on a C1 Single Cell Auto Prep System (Fluidigm) using the C1 Single-Cell mRNA seq HT Reagent Kit v2 (Fluidigm). After initial cell capture, the IFC was scanned on a Leica DMI6000B microscope to verify cell capture efficiency. Cell lysis, reverse transcription, PCR amplification, cell bar code tagging, and harvesting was done onboard the C1 System. Harvested sample cleanup was performed using AMPure XP beads (Beckman Coulter, Brea, CA).
Sequencing libraries were generated using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA), with indexes from Nextera XT Index Primer Set A and Set B. Libraries were pooled and library quality was accessed on an Agilent High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA).
The pooled library, combined with 30% PhiX, was loaded on a Nextseq 500/550 High Output Kit v2 Flowcell (Illumina) and sequenced on a Nextseq 500 Sequencing System (Illumina) using paired end reads (R1-26bp, R2–120bp).

tag: cell population

value: CD31- CD45- E-cadherin+ tdTomato+

value: Alveolar type 1


title: 8-Control


title: 2-Treatment


title: Control female 1


title: 12-Control


title: scRNA-seq: COL19_ROW39


title: 5-Treatment


title: scRNA-seq: COL19_ROW35


title: scRNA-seq: COL19_ROW38


title: SCO_+D_rep2


title: scRNA-seq: COL20_ROW30


title: ACO_rep1


title: 4-Control


title: scRNA-seq: COL19_ROW05


title: scRNA-seq: COL18_ROW36


title: scRNA-seq: COL20_ROW17


title: scRNA-seq: COL18_ROW33


title: scRNA-seq: COL18_ROW40


title: scRNA-seq: COL17_ROW23


title: scRNA-seq: COL17_ROW10


title: scRNA-seq: COL18_ROW34


title: scRNA-seq: COL18_ROW19


title: scRNA-seq: COL16_ROW40


title: scRNA-seq: COL17_ROW34


title: scRNA-seq: COL19_ROW17


title: scRNA-seq: COL17_ROW01


title: scRNA-seq: COL17_ROW02


title: scRNA-seq: COL18_ROW29


title: scRNA-seq: COL18_ROW38


title: scRNA-seq: COL19_ROW20


title: scRNA-seq: COL17_ROW29


title: scRNA-seq: COL16_ROW35


title: scRNA-seq: COL16_ROW06


title: P1M4: pancreas_risperidone_male 4

value: pancreas

value: risperidone 1 mg/kg

value: male


title: scRNA-seq: COL15_ROW36


title: scRNA-seq: COL15_ROW27


title: scRNA-seq: COL18_ROW35


title: scRNA-seq: COL16_ROW27


title: scRNA-seq: COL16_ROW11


title: scRNA-seq: COL16_ROW20


title: scRNA-seq: COL16_ROW30


title: scRNA-seq: COL15_ROW06


title: scRNA-seq: COL15_ROW28


title: scRNA-seq: COL13_ROW23


title: scRNA-seq: COL12_ROW33


title: scRNA-seq: COL15_ROW24


title: scRNA-seq: COL16_ROW21


title: scRNA-seq: COL11_ROW32


title: scRNA-seq: COL16_ROW25


title: scRNA-seq: COL11_ROW26


title: scRNA-seq: COL14_ROW36


title: scRNA-seq: COL13_ROW35


title: scRNA-seq: COL14_ROW13


title: scRNA-seq: COL15_ROW16


title: scRNA-seq: COL11_ROW23


title: scRNA-seq: COL11_ROW20


title: scRNA-seq: COL13_ROW34


title: scRNA-seq: COL16_ROW08


title: scRNA-seq: COL13_ROW25


title: scRNA-seq: COL15_ROW40


title: scRNA-seq: COL12_ROW27


title: scRNA-seq: COL13_ROW17


title: scRNA-seq: COL12_ROW11


title: scRNA-seq: COL15_ROW15


title: scRNA-seq: COL12_ROW10


title: scRNA-seq: COL10_ROW30


title: scRNA-seq: COL10_ROW19


title: scRNA-seq: COL12_ROW06


title: scRNA-seq: COL12_ROW08


title: scRNA-seq: COL12_ROW03


title: scRNA-seq: COL10_ROW35


title: scRNA-seq: COL11_ROW33


title: scRNA-seq: COL11_ROW40


title: scRNA-seq: COL09_ROW25


title: scRNA-seq: COL10_ROW06


title: scRNA-seq: COL09_ROW32


title: scRNA-seq: COL12_ROW19


title: scRNA-seq: COL11_ROW25


title: scRNA-seq: COL11_ROW38


title: scRNA-seq: COL09_ROW04


title: scRNA-seq: COL09_ROW12


title: scRNA-seq: COL11_ROW15


title: scRNA-seq: COL11_ROW10


title: scRNA-seq: COL10_ROW24


title: scRNA-seq: COL11_ROW16


title: scRNA-seq: COL10_ROW14


title: scRNA-seq: COL14_ROW07


title: scRNA-seq: COL10_ROW39


title: scRNA-seq: COL09_ROW33


title: scRNA-seq: COL08_ROW28


title: PCM19: pancreas_control_male 19


title: scRNA-seq: COL08_ROW21


title: scRNA-seq: COL09_ROW24


title: scRNA-seq: COL09_ROW23


title: scRNA-seq: COL07_ROW19


title: scRNA-seq: COL07_ROW01


title: scRNA-seq: COL07_ROW06


title: scRNA-seq: COL09_ROW03


title: scRNA-seq: COL08_ROW30


title: scRNA-seq: COL08_ROW31


title: scRNA-seq: COL07_ROW36


title: scRNA-seq: COL07_ROW12


title: scRNA-seq: COL07_ROW13


title: scRNA-seq: COL07_ROW17


title: scRNA-seq: COL07_ROW29


title: scRNA-seq: COL08_ROW14


title: scRNA-seq: COL07_ROW31


title: scRNA-seq: COL07_ROW07


title: scRNA-seq: COL08_ROW01


title: scRNA-seq: COL05_ROW05


title: scRNA-seq: COL06_ROW39


title: scRNA-seq: COL04_ROW20


title: scRNA-seq: COL06_ROW35


title: scRNA-seq: COL04_ROW03


title: scRNA-seq: COL04_ROW04


title: scRNA-seq: COL03_ROW37


title: scRNA-seq: COL06_ROW25


title: scRNA-seq: COL08_ROW17


title: scRNA-seq: COL06_ROW30


title: scRNA-seq: COL06_ROW32


title: scRNA-seq: COL06_ROW08


title: scRNA-seq: COL05_ROW34


title: scRNA-seq: COL06_ROW24


title: scRNA-seq: COL03_ROW23


title: scRNA-seq: COL05_ROW27


title: scRNA-seq: COL06_ROW03


title: scRNA-seq: COL03_ROW11


title: scRNA-seq: COL04_ROW39


title: scRNA-seq: COL04_ROW36


title: scRNA-seq: COL04_ROW06


title: scRNA-seq: COL03_ROW07


title: scRNA-seq: COL03_ROW30


title: scRNA-seq: COL02_ROW37


title: scRNA-seq: COL02_ROW36


title: scRNA-seq: COL02_ROW28


title: scRNA-seq: COL02_ROW27


title: scRNA-seq: COL03_ROW05


title: scRNA-seq: COL03_ROW02


title: scRNA-seq: COL02_ROW24


title: scRNA-seq: COL02_ROW06


title: scRNA-seq: COL01_ROW08


title: scRNA-seq: COL02_ROW18


title: scRNA-seq: COL02_ROW01


title: scRNA-seq: COL01_ROW37


title: DU145_HA_HNF1B_HA

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg19  genome assembly using bowtie (version 1.0.0)
peaks were called using macs14 with the following setting: --pvalue=1e-5, --nomodel
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using macs14

source_name: DU145 cell line

growth_protocol: DU145 cells were maintain in RPMI-1640 supplemented with 10% FBS and antibiotics (100 units/ml penicillin and 0.1 mg/ml streptomycin)

extract_protocol:
DU145 cells were crosslinked with 1% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M glycine, then collected and suspended in ChIP lysis buffer (50 mM HEPES-NaOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton, 0.05% SDS, 0.1% sodium deoxycholate with freshly added proteinase inhibitor, and PMSF) for sonication. Sonicated lysate was incubated with HA antibody (3724S, Cell Signaling Technology) overnight at 4 ℃, and additionally with protein A/G agarose beads (SA032005, Smart-lifesciences) for 1h. The protein-DNA complex was washed and ChIP'ed DNA was purified by PCR purification kit (28106,  QIAGEN).
Libraries were prepared by Accel-NGS 2S Plus DNA library kit (Swift, 21096)

value: prostate cancer cell line

value: overexpressing HA tagged HNF1B

tag: chip antibody


title: scRNA-seq: COL01_ROW40


title: scRNA-seq: COL01_ROW01


title: p1_RNA

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

institute: Fifth Medical Center of Chinese PLA General Hospital

data_processing:
10X Genomics CellRanger version 3.0.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 3.0.1) with default mapping arguments.
After quality control, UMI data was subjected to Scanpy (version 1.5.1) for analyses.
Differentially expressed genes were identified using the Wilcox method implemented by ‘FindMarkers’ or ‘FindAllMarkers’ functions in Seurat (version 3.2.2).
Scirpy package was used to analyze our TCR sequencing data.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: Peripheral blood

extract_protocol: Chromium Single cell 3’ and 5' Library and Gel Bead Kit V3 (10X Genomics) was used for scRNA-seq and TCR sequences libraries construction

tag: individual

value: T cells

tag: facs antibody

tag: disease state

value: B cell-acute lymphoblastic leukemia


title: p2_TCR

data_processing:
Library strategy: TCR-Seq
10X Genomics CellRanger version 3.0.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 3.0.1) with default mapping arguments.
After quality control, UMI data was subjected to Scanpy (version 1.5.1) for analyses.
Differentially expressed genes were identified using the Wilcox method implemented by ‘FindMarkers’ or ‘FindAllMarkers’ functions in Seurat (version 3.2.2).
Scirpy package was used to analyze our TCR sequencing data.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell


title: DU145_HA_HNF1B_Input


title: p1_TCR


title: scRNA-seq: COL01_ROW27


title: scRNA-seq: COL03_ROW08


title: p3_TCR


title: scRNA-seq: COL02_ROW39


title: p2_RNA


title: h2_RNA

value: healthy individual


title: p3_RNA


title: Interacting S.co WT -rep3 (2017)

city: Berkeley

first: Matthew

middle: F

last: Traxler

state: CA

address: 311 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

data_processing:
Reads were cleaned and trimmed using trimmomatic version 0.33.0
mapping to the genome was done using bowtie2 version 2.2.4.1
reads were counted with HTSeq version 0.11.3
differential expression was tested using DESeq2 version 1.26.0 on R version 3.6.3
Genome_build: Streptomyces coelicolor A3(2) complete genome AL645882
Supplementary_files_format_and_content: tab-delimited text file with the read counts for each gene

organism: Streptomyces coelicolor

source_name: Bacterial patches

growth_protocol: 0.5ul of a 2x10^8 cfu/ml Streptomyces coelicolor spore stock was spotted on ~2mm think  ISP2 agar plates and grown at 30C for 4 days

extract_protocol:
Biomass was scraped off agar plates and frozen in liquid nitrogen followed by grinding with mortar and pestle and addition of trizol. The Zymogen Direct-zol RNA miniprep kit (R2051) was used to purify the RNA, with the optional DNase treatment step included
RNA preparation was done by the UC Berkeley Functional Genomics Laboratory. Briefly, rRNA was removed using the Illumina Ribo-Zero rRNA removal kit (bacteria) and the remaining RNA was prepared with a Wafergen PrepX RNA library prep kit for Illumina. Indexing PCR was performed using in-house dual indexed primers and 14 cycles.

treatment_protocol: Interacting patches had 0.5ul of a 8x10^8 Amycolatopsis sp. AA4 stock spotted 0.75cm away

value: WT

value: interacting


title: Interacting S.co ΔcvnA8 -rep3 (2017)

value: {delta}SCO6943 (cvnA8)


title: Interacting S.co ΔcvnF8 -rep2 (2017)

value: {delta}SCO6939 (cvnF8)


title: Interacting S.co ΔcvnF8 -rep3 (2017)


title: Interacting S.co ΔcvnA8 -rep2 (2017)


title: Interacting S.co WT -rep2 (2017)


title: Interacting S.co WT -rep1 (2017)


title: Isolated S.co ΔcvnA8 -rep3 (2017)

value: isolated


title: Isolated S.co ΔcvnF8 -rep1 (2017)


title: Isolated S.co ΔcvnF8 -rep3 (2017)


title: HEK293T cells, shLATS1B

city: Suzhou

first: Yibo

last: Zuo

address: Renai road 199

institute: Soochow university

data_processing:
Illumina Casava1.7 software used for basecalling.
Genome_build: NCBI (GCF_000001405.39_GRCh38.p13)
Supplementary_files_format_and_content: gene_expression.txt (fpkm, tpm, read count)
Supplementary_files_format_and_content: Up_and_down_Top_20_genes.xls (Select the top 20 genes with the highest degree of up-regulation and down-regulation for analysis)

extract_protocol:
HEK293T cells were transfected with either control shRNAs (shCON) or shRNAs against LATS1 (shLATS1) and then treated with IFNα (1,000 IU/ml) for 4 hrs. Total RNAs were isolated from HEK293T cells using TRIzol reagent (Invitrogen). The RNA samples were sent to Wuhan BGI for further sequencing and analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LATS1 knockdown


title: Isolated S.co ΔcvnF8 -rep2 (2017)


title: Isolated S.co WT -rep1 (2017)


title: Isolated S.co WT -rep2 (2017)


title: HEK293T cells, CON3

value: control


title: Isolated S.co ΔcvnA8 -rep2 (2017)


title: Isolated S.co WT -rep3 (2017)


title: HEK293T cells, shLATS1C


title: HEK293T cells, CON2


title: Interacting S.co ΔcvnA8 -rep1 (2017)


title: Interacting S.co ΔcvnF8 -rep1 (2017)


title: mutant NSC passage 2 #3

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

country: South Korea

institute: Chungnam National University

description: mLRRK2-NSC-P2 #3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2.
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Neural Stem Cell

growth_protocol: iPSCs were incubated for 6 h in DMEM/F12 supplemented with 2% B27 (without vitamin A), 1% N-2 , 10 μM Y-27632 , 500 ng/ml noggin , 20 μM SB431542 , and 2 ng/ml bFGF in non-adherent conditions. Cells were plated on poly-ornitin/laminin coated dishes and cultured for 10 days in the same medium as above. On day 11, cells were detached mechanically, re-plated on poly ornitin/laminin-coated dishes, and cultured in neural induction medium containing 50% DMEM/F12, 50% neurobasal medium supplemented with 2% B27, 1% N-2, 0.5% Glutamax, 10 ng/ml epidermal growth factor, and 10 ng/ml bFGF.

extract_protocol:
Total RNA was extracted from the cell pellets using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
Libraries were prepared according to TruSeq Stranded Total RNA LT sample prep kit (Gold). Briefly, Genomic DNA was removed by Dnase treatment. RNA was purified by ribo-zero rRNA removal kit. The purified RNAs were fragmented to do sequencing by short read. The cDNAs were synthesized from the fragmented RNA, and then were ligated with adapter in the flanking ends. The aquisition of insert ranging 200-400 bp was sequenced through paired-end sequencing.

treatment_protocol: nontreatment

value: iPSC-derived neural stem cell

value: LRRK2 G2021S

value: Parkinson's disease

tag: passages

value: passage 2


title: HEK293T cells, shLATS1A


title: mutant NSC passage 13

value: LRRK2 G2020S

value: passage 13


title: mutant NSC passage 2 #1

description: mLRRK2-NSC-P2 #1

value: LRRK2 G2019S


title: correction NSC passage 2 #1

description: cLRRK2-NSC-P2 #1

value: normal LRRK2

value: normal


title: correction NSC passage 2 #3

description: cLRRK2-NSC-P2 #3

value: normal LRRK4


title: correction NSC passage 2 #2

description: cLRRK2-NSC-P2 #2

value: normal LRRK3


title: mutant NSC passage 1

value: passage 1


title: HEK293T cells, CON1


title: correction NSC passage 13


title: scRNA-seq: COL03_ROW29

value: CD31- CD45- E-cadherin+ tdTomato+

value: Alveolar type 1


title: correction NSC passage 1


title: SiCTR CHLA-Med #3

city: Rome

first: Silvia

last: Campello

state: <None>

address: Via della Ricerca Scientifica

department: Department of Biology

institute: University of Rome, Tor Vergata

data_processing:
Fastq files were uploded on Base Space Sequence Hub (Illumina, San Diego, CA, USA) and DRAGEN RNA pipeline and DRAGEN differential expression apps were launched for reads quality check, hg38 alignment and differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: raw count obtein with featureCount

source_name: CHLA-Med cells

growth_protocol: DMEM-F12 supplemented with B27, EGF and FGF

extract_protocol:
total RNA extraction using a Qiagen RNeasy Kit
RNA concentration was tested by Qubit RNA Assay Kit in Qubit Fluorometer and its integrity analyzed with Agilent 4150 Bioanalyzer. Indexed libraries were prepared from 100ng/ea of purified RNA with Illumina® RNA Prep, Tagmentation (L) with Enrichment kit (Exome Panel) (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

treatment_protocol: RNA interference was performed using Lipofectamine RNAiMAX reagent in accordance with the manufacturer’s instructions

value: CHLA-Med cells

value: Medulloblastoma

value: Ctr condition


title: renal cell carcinoma tissue_rep1

city: hangzhou

first: Lifeng

last: Ding

state: zhejiang

address: qingchun dong road 3#

department: department of urology

institute: Zhejiang university school of medcine sir run run shaw hosptial

data_processing:
Sequencing quality was examined by FastQC software
trimmed reads (pass Illumina quality filter, trimmed 3'-adaptor bases by cutadapt) were aligned to the piRBase (a manually curated resource of piRNAs) using NovoAlign software (v2.07.11)
The expression profiling and differential expression of piRNAs were calculated based on normalized TPM
R or Perl environment for statistical computing and graphics
Genome_build: hg18
Supplementary_files_format_and_content: Matrix table with raw gene counts for every piRNA and every sample

source_name: Human renal tissues

extract_protocol:
TRIzol reagent was used to extract RNA from tissues
Total RNA of each sample was used to prepare the piRNA-sequencing library, which included the following steps: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~142-153bp PCR amplified fragments (corresponding to ~24-35 nt small RNAs). The libraries are qualified and quantified using Agilent BioAnalyzer2100.
piRNA sequencing

value: renal cell carcinoma tissue


title: h1_RNA

city: Beijing

value: T cells

value: healthy individual


title: adjacent normal tissue_rep2

value: adjacent normal tissue


title: renal cell carcinoma tissue_rep2


title: adjacent normal tissue_rep1


title: SiAMBRA1 CHLA-Med #2

value: RNA interference for AMBRA1


title: mutant NSC passage 2 #2

description: mLRRK2-NSC-P2 #2

value: iPSC-derived neural stem cell

value: LRRK2 G2020S

value: Parkinson's disease

value: passage 2


title: SiAMBRA1 CHLA-Med #1


title: SiATG7 #3

data_processing:
The raw sequence files generated (.fastq files) underwent quality control analysis using FastQC Fastq underwent Quality Control using FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The mapping of paired-end reads was performed using STAR (version 2.5.2a)72 on reference genome assembly hg19 obtained from Ensembl (GRCh37.p13)73 (https://grch37.ensembl.org/Homo_sapiens/Info/Index
The quantification of transcripts expressed for each sample was performed using FeatureCount algorithm.
DESeq2 was used to normalize the data and then to perform the differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: raw count obtein with featureCount

source_name: D283-Med cells

growth_protocol: Eagle's Minimum Essential Medium supplemented with FBS 10%

extract_protocol:
total RNA extraction using a Qiagen RNeasy Kit
RNA concentration in each sample was assayed with a ND-1000 spectrophotometer (NanoDrop) and its quality assessed with the Agilent Tapestation 4200 (Agilent Technologies). Indexed libraries were prepared from 1 ug/ea purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions

value: D283-Med cells


title: SiATG7 #1


title: SiATG7 #2


title: SiAMBRA1 #2


title: SiCTR #1


title: SiCTR #2


title: scRNA-seq: COL03_ROW12


title: SiAMBRA1 #1


title: SiAMBRA1 #3


title: SiCTR CHLA-Med #1


title: SiCTR #3


title: SiAMBRA1 CHLA-Med #3


title: SiCTR CHLA-Med #2


title: LS-14684_S39_E1-50

city: Seattle

first: Bosiljka

last: Tasic

state: WA

address: 615 Westlake Ave N.

department: Molecular Genetics

institute: Allen Institute for Brain Science

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: mm10, Mmul_10

source_name: Mouse LGN - Shell

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia. The brain tissues of two adult M. nemestrina (southern pig-tailed macaque) and one M. fascicularis  (crab-eating macaque) were obtained through the Tissue Distribution Program of the Washington  National Primate Research Center and conformed to the guidelines provided by the US National  Institutes of Health. All procedures were approved by the Institutional Animal Care and Use Commit-  tee of the University of Washington under protocol number 4277-01.

extract_protocol:
We isolated single cells and nuclei as previously described (Tasic et al., 2016, Bakken et al., 2018) with modifications. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C. For nuclei isolation, dissected regions of interest were transferred to microcentrifuge tubes, snap frozen in a slurry of dry ice and ethanol, and stored at -80°C until the time of use. To isolate nuclei, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin Plus RNase inhibitor (Promega), 1X protease inhibitor (Promega), and 0.1mM DTT. Tissues were placed into a 1ml dounce homogenizer (Wheaton) and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer (Miltenyi Biotech) and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in staining buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

tag: donor

tag: Sex

value: M

value: dLGN - Shell

tag: facs gating

value: RFP-positive

tag: sequencing batch

tag: cell class

value: Glut

tag: cell cluster

value: LGd


title: LS-14684_S44_E1-50

value: GABA


title: LS-14684_S36_E1-50


title: LS-14684_S48_E1-50


title: LS-14684_S38_E1-50


title: LS-14684_S46_E1-50


title: LS-14684_S37_E1-50


title: LS-14684_S45_E1-50


title: LS-14684_S40_E1-50


title: LS-14684_S47_E1-50


title: LS-14684_S41_E1-50


title: LS-14684_S43_E1-50


title: h2_TCR


title: LS-14684_S33_E1-50

value: Non-Neuronal


title: LS-14684_S31_E1-50

value: Low Quality


title: LS-14684_S32_E1-50


title: LS-14684_S34_E1-50


title: LS-14684_S26_E1-50


title: LS-14684_S27_E1-50


title: LS-14684_S30_E1-50


title: LS-14684_S28_E1-50


title: Isolated S.co ΔcvnA8 -rep1 (2017)

value: {delta}SCO6943 (cvnA8)

tag: treatment

value: isolated


title: LS-14684_S29_E1-50


title: LS-14684_S16_E1-50


title: LS-14684_S35_E1-50


title: LS-14684_S12_E1-50


title: LS-14684_S15_E1-50


title: LS-14684_S13_E1-50


title: LS-14684_S25_E1-50


title: LS-14684_S10_E1-50


title: LS-14684_S07_E1-50


title: LS-14684_S08_E1-50


title: LS-14684_S14_E1-50


title: LS-14684_S09_E1-50


title: LS-14684_S02_E1-50


title: LS-14684_S01_E1-50


title: LS-14684_S05_E1-50


title: LS-14684_S04_E1-50


title: LS-14684_S11_E1-50


title: LS-14680_S96_E1-50


title: LS-14680_S95_E1-50


title: LS-14684_S06_E1-50


title: LS-14680_S92_E1-50


title: LS-14680_S93_E1-50


title: LS-14680_S91_E1-50


title: LS-14680_S87_E1-50


title: LS-14684_S03_E1-50


title: LS-14680_S94_E1-50


title: LS-14680_S90_E1-50


title: LS-14680_S89_E1-50


title: LS-14680_S88_E1-50


title: LS-14680_S84_E1-50


title: LS-14680_S83_E1-50


title: LS-14680_S82_E1-50


title: LS-14680_S86_E1-50


title: LS-14680_S85_E1-50


title: LS-14680_S79_E1-50


title: LS-14680_S80_E1-50


title: LS-14680_S81_E1-50


title: LS-14680_S78_E1-50


title: LS-14680_S71_E1-50


title: LS-14680_S72_E1-50


title: LS-14680_S77_E1-50


title: LS-14680_S76_E1-50


title: LS-14680_S74_E1-50


title: LS-14680_S75_E1-50


title: LS-14680_S64_E1-50


title: LS-14680_S69_E1-50


title: LS-14680_S68_E1-50


title: LS-14680_S66_E1-50


title: LS-14680_S70_E1-50


title: LS-14680_S65_E1-50


title: LS-14680_S67_E1-50


title: LS-14680_S73_E1-50


title: LS-14680_S59_E1-50


title: LS-14680_S63_E1-50


title: LS-14680_S62_E1-50


title: LS-14680_S58_E1-50


title: LS-14680_S61_E1-50


title: LS-14680_S57_E1-50


title: LS-14680_S56_E1-50


title: LS-14680_S55_E1-50


title: LS-14680_S54_E1-50


title: LS-14680_S52_E1-50


title: LS-14680_S53_E1-50


title: LS-14680_S49_E1-50


title: LS-14680_S50_E1-50


title: LS-14680_S51_E1-50


title: LS-14680_S47_E1-50


title: LS-14680_S48_E1-50


title: LS-14680_S60_E1-50


title: LS-14680_S41_E1-50


title: LS-14680_S40_E1-50


title: LS-14680_S45_E1-50


title: LS-14680_S38_E1-50


title: LS-14680_S36_E1-50


title: LS-14680_S37_E1-50


title: LS-14680_S42_E1-50


title: LS-14680_S35_E1-50


title: LS-14680_S31_E1-50


title: LS-14680_S33_E1-50


title: LS-14680_S30_E1-50


title: LS-14680_S32_E1-50


title: LS-14680_S26_E1-50


title: LS-14680_S46_E1-50


title: LS-14680_S43_E1-50


title: LS-14680_S44_E1-50


title: LS-14680_S28_E1-50


title: LS-14680_S29_E1-50


title: LS-14680_S39_E1-50


title: LS-14680_S34_E1-50


title: LS-14680_S24_E1-50


title: LS-14680_S25_E1-50


title: LS-14680_S17_E1-50


title: LS-14680_S08_E1-50


title: LS-14680_S21_E1-50


title: LS-14680_S18_E1-50


title: LS-14680_S19_E1-50


title: LS-14680_S05_E1-50


title: LS-14680_S22_E1-50


title: LS-14680_S23_E1-50


title: LS-14680_S04_E1-50


title: LS-14680_S20_E1-50


title: LS-14680_S02_E1-50


title: LS-14680_S07_E1-50


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source_name: Mouse LGv

value: LGv


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