title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_18


title: lung single cell 22

status: Public on May 11 2022

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description:
lung single cell 22
898s_A7

library_source: transcriptomic

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
A 12 week-old female Prox1-GFP mouse was perfused with PBS to clear the blood. Subsequently, the lung was filled with 10 mg mL-1 dispase II in PBS via the trachea and incubated for 10 min at RT. Next, 1.0 mg mL-1 collagenase II in PBS supplemented with 0.2 mg mL-1 DNase I was injected into the lung lobes and lung tissue was minced with scissors in 1.5 mL of 1.0 mg mL-1 collagenase II in PBS supplemented with 0.2 mg mL-1 DNase I. Tissue dissociation was performed for 15 min at 37°C and 750 rpm. Digests were quenched by the addition of 2 mM EDTA f.c., filtered through a 40 µm nylon filter, washed with FACS buffer (PBS, 0.5% FBS, and 2 mM EDTA) for 5 min at 300 g, RT and processed for FACS sorting. Briefly,  Fc-receptor binding was blocked with rat anti-mouse CD16/CD32 for 10 min on ice. Thereafter, samples were incubated with fluorophore-conjugated anti-CD31 (clone 390, 1.0 µg mL-1), anti-CD45 (clone 30-F11, 4 µg mL-1), anti-CD11b (clone M1/70, 4 µg mL-1) and anti-TER-119 (clone TER-119, 4 µg mL-1) antibodies for 20 min on ice. Prior to sorting of CD31+ Prox1-GFP+ CD45- CD11b- Ter119- lymphatic and CD31+ Prox1-GFP- CD45- CD11b- Ter119- blood endothelial cells on a BD FACS Aria III samples were again filtered through a 40 µm filter and supplemented with 1 µM SytoxBlue to label dead cells.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: lung

tag: age

value: adult mice

tag: genotype


title: fasted-BAT21

type: RNA

city: Graz

first: Ingeborg

last: Klymiuk

address: Neue Stiftingtalstrasse 6

country: Austria

institute: Medical Univ Graz

hyb_protocol: Affymetrix Mouse Gene 2.0 ST Array (Cat No. 902118);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);  Affymetrix Genechip® fluidics station 450: protocol FS450_0002 (7) for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 3.2.)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.

source_name: brown adipose tissue

label_protocol: Affymetrix WT PLUS Reagent Kit P/N 703147 Rev3, (Cat No. 902280); Lot: 4248402

extract_protocol: Qiagen microRNAEasy

tag: tag

tag: groupt

value: fasted


title: refed-BAT15

value: refed


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_17

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
The RNA-seq reads were aligned using HISAT2
Genes that are expressed (read counts > 0) in at least one replicate in both control and ECKO are included for analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR
WGBS reads were aligned with BS Seeker 2.  CG sites with read depth >= 4 are preserved in the Cgmap.gz file.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files includes RPKM values for each sample.

molecule: polyA RNA

source_name: Primordial germ cells

growth_protocol: Control and ECKO male and female embryos were obtained from crosses between OG; Eedfl/fl (Lengner et al., 2007; Yu et al., 2009) homozygous females and BC; Eedf/l+ heterozygous males (Ohinata et al., 2005) at E10.5, E11.5 and E13.5. Embryos were staged by the detection of a vaginal plug on the morning after time-mating pairs were established E0.5.

extract_protocol:
Female E12.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific).
Single Cell RNA sequencing libraries were prepared according to the Smart Seq 2 single cell sequencing protocol (Picelli et al., 2014). The RNA was converted to cDNA in each well using Superscript II (Invitrogen). The cDNA was amplified in each well using a KAPA HiFI HotStart polymerase (KAPA Biosystems) in a PCR run for 18 cycles. cDNA was tagged via the Nextera Tagmentation kit (Illumina) using libraries A and C (Illumina). Indexed cDNA was pooled and run on a 2% agarose gel and the smear between 200-500 bp was extracted. Gel extract was cleaned with the Qiagen Gel Extraction Kit (Qiagen) and sent for sequencing.

tag: cell type

value: Primordial germ cells

tag: developmental stage

value: Eed -/-

tag: gender

value: Female


title: SOK6_Rep2l_0Gy_48h

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Genome_build: hg38
Supplementary_files_format_and_content: Rsubreads raw counts per HGNC symbol in text files

organism: Homo sapiens

source_name: OKF6 cell line

extract_protocol:
Total RNA was extracted using Nucleospn RNA extraction kit from Macherey & Nagel
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: replicate

tag: time

tag: treatment irradiation

value: oral ketratinocytes

tag: hpv-status

value: HPV-negative


title: fed-BAT45

value: fed


title: fasted-BAT33


title: lung single cell 21

description:
lung single cell 21
898s_A6


title: fasted-BAT17


title: paperCLIP_cTag_NP_3

city: New York

first: Caryn

middle: R

last: Hale

state: New York

address: 1230 York Avenue

country: USA

institute: Rockefeller University

data_processing:
Library strategy: PAPERCLIP
filtering and demultiplexing using fastq_filter.pl (CTK package, Zhang lab, min:0-15:20,mean:16-41:20)
trim 3' linker sequence using cutadapt (AAAAAAAAAAAAAAAAAAAATCTCGTATGCCGTCTTCTGCTTG)
collapse exact duplicates using fastq2collapse.pl (CTK package, Zhang lab)
trim 5' barcode and linker using stripBarcode.pl (CTK package, Zhang lab)
alignment with novoalign without trimming.  A minimum of 25 nt match to genome was required.
collapse PCR duplicates using tag2collapse.pl (CTK package, Zhang lab)
tags were overlapped with peaks determined by previously published Camk2a cTag-PAPERCLIP data (hwang et al, 2017)
Genome_build: mm10

source_name: Microdissected hippocampus CA1

extract_protocol:
Microdissection was performed on hippocampal slices UV-crosslinked in HBSS. Tissue was homogenized in lysis buffer (1x PBS, 0.1% SDS, 0.5% NP-40, 0.5% Sodium deoxycholate supplemented, 1X cOmplete Mini EDTA-free Protease Inhibitor (Roche)) by passing through syringes with a 28 gauge needle. cTag-PAPERCLIP was performed as described previously (see associated paper for details).
RNA tags were cloned using the BrdU-CLIP and cTag-PAPERCLIP method as described in associated paper.

value: Microdissected hippocampus CA1

value: Camk2a-Cre x Pabpc1- cTag

tag: region

value: CA1 neuropil

tag: labeled protein

tag: sample type

value: CLIP tag (RNA)


title: fed-BAT3


title: lung single cell 20

description:
lung single cell 20
898s_A5


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_20


title: paperCLIP_cTag_NP_2


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_19


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_21


title: S154_Rep2l_0Gy_48h

source_name: UPCI:SCC154 cell line

value: head and neck squamous cell carinoma (HNSCC)

value: HPV-positive


title: lung single cell 19

description:
lung single cell 19
898s_A4


title: paperCLIP_cTag_NP_1


title: S2_Rep2l_0Gy_72h

source_name: UD-SCC2 cell line


title: paperCLIP_cTag_NP_4


title: S99_Rep2l_0Gy_48h

source_name: UPCI:SCC099 cell line


title: lung single cell 18

description:
lung single cell 18
898s_A3


title: S131_Rep2l_0Gy_48h

source_name: UPCI:SCC131 cell line


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_23


title: FMRP_cTag_NP_CLIP_4

data_processing:
Library strategy: FMRP-CLIP
filtering and demultiplexing using fastq_filter.pl (CTK package, Zhang lab, min:0-15:20,mean:16-41:20)
trim 3' linker sequence using cutadapt (GTGTCAGTCACTTCCAGCGG)
collapse exact duplicates using fastq2collapse.pl (CTK package, Zhang lab)
trim 5' barcode and linker using stripBarcode.pl (CTK package, Zhang lab)
alignment with STAR to refseq mm10 transcriptome
collapse PCR duplicates using tag2collapse.pl (CTK package, Zhang lab)
selected most abundant transcript per gene, removed multimapped reads and reads not mapping in the appropriate direction in the transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: tags_per_transcript_FMRP_cTag_CB_NP_CLIP.txt, Microdissected CAmk2a-FMRP cTag reads mapped to CA1 transcripts

extract_protocol:
Microdissection was performed on hippocampal slices UV-crosslinked in HBSS with 0.1 mg/mL cycloheximide. Tissue was homogenized in lysis buffer (1x PBS, 0.1% SDS, 0.5% NP-40, 0.5% Sodium deoxycholate supplemented, 1X cOmplete Mini EDTA-free Protease Inhibitor (Roche) and 0.1 mg/mL cycloheximide) by passing through syringes with a 28 gauge needle. cTag FMRP-CLIP was performed as described previously (see associated paper for details).
RNA tags were cloned using the BrdU-CLIP method as described in associated paper.

value: Camk2a-Cre x Fmr1 cTag

value: FMRP


title: lung single cell 17

description:
lung single cell 17
898s_A2

value: lung

value: adult mice


title: FMRP_cTag_NP_CLIP_5


title: S40_Rep2l_0Gy_48h

source_name: UPCI:SCC040 cell line


title: fed-BAT23


title: FMRP_cTag_NP_CLIP_3


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_22


title: lung single cell 16

description:
lung single cell 16
898s_A24


title: S27_Rep2_0Gy_48h

source_name: Cal27 cell line


title: lung single cell 15

description:
lung single cell 15
898s_A23


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_24


title: lung single cell 14

description:
lung single cell 14
898s_A22


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_1


title: S2_Rep2l_0Gy_48h


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_2


title: SOK6_Rep1e_8Gy_4h_X

value: 8 Gy X-ray


title: FMRP_cTag_NP_CLIP_1


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_4

value: Primordial germ cells


title: lung single cell 13

description:
lung single cell 13
898s_A21


title: lung single cell 12

description:
lung single cell 12
898s_A20


title: FMRP_cTag_CB_CLIP_5

value: CA1 cell bodies layer


title: S154_Rep1e_8Gy_4h_X


title: FMRP_cTag_CB_CLIP_4


title: lung single cell 11

description:
lung single cell 11
898s_A1


title: S33_Rep2l_0Gy_48h

source_name: Cal33 cell line


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_5

value: Eed -/-

value: Female


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_3


title: S131_Rep1e_8Gy_4h_X

value: HPV-negative


title: FMRP_cTag_CB_CLIP_2


title: S99_Rep1e_8Gy_4h_X


title: FMRP_cTag_CB_CLIP_3


title: FMRP_cTag_NP_CLIP_2


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_7


title: S40_Rep1e_8Gy_4h_X


title: FMRP_cTag_CB_CLIP_1


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_6


title: S33_Rep1e_8Gy_4h_X


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_8


title: lung single cell 8

description:
lung single cell 8
898s_A17


title: lung single cell 7

description:
lung single cell 7
898s_A16


title: S27_Rep1e_8Gy_4h_X


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_17

value: Male


title: lung single cell 6

description:
lung single cell 6
898s_A15


title: SOK6_Rep1e_4Gy_4h_X

value: 4 Gy X-ray

value: oral ketratinocytes


title: KYSE30 cells, ACh-stimulated, 4Hours [KA1001]

city: Nanjing

first: Bin

last: Wei

state: Jiangsu

address: 101 Longmian Avenue

country: China

institute: Nanjing medical university

data_processing:
Illumina Casava1.7 software
Trimmed sequence reads were mapped to mm8 using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size（RPKM）were calculated using a protocol from chepelev et，al.Nucleic Acids Research,2009.In short ,axons from all iso forms.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: KYSE30  cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: KYSE30 cells were induced by treatment of 4 hours  with 100uM ACH  (Sigma),

tag: cell line

value: Esophageal squamous cell carcinoma cell

value: WT

tag: treatment

value: ACh-stimulated


title: lung single cell 10

description:
lung single cell 10
898s_A19

tag: strain

tag: tissue


title: lung single cell 5

description:
lung single cell 5
898s_A14

tag: age

tag: genotype


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_20


title: KYSE30 cells, ACh-stimulated, 4Hours [KA1002]


title: KYSE30 cells, Control, 4Hours [K3]

value: Control


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_18


title: lung single cell 4

description:
lung single cell 4
898s_A13


title: lung single cell 9

description:
lung single cell 9
898s_A18


title: lung single cell 3

description:
lung single cell 3
898s_A12


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_21


title: S131_Rep1e_4Gy_4h_X

value: head and neck squamous cell carinoma (HNSCC)


title: KYSE30 cells, Control, 4Hours [K2]


title: S99_Rep1e_4Gy_4h_X


title: KYSE30 cells, Control, 4Hours [K1]


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_19


title: KYSE30 cells, ACh-stimulated, 4Hours [KA1003]


title: S40_Rep1e_4Gy_4h_X


title: lung single cell 2

description:
lung single cell 2
898s_A11


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_22


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_23


title: S33_Rep1e_4Gy_4h_X


title: lung single cell 1

description:
lung single cell 1
898s_A10


title: S154_Rep1e_4Gy_4h_X

value: HPV-positive


title: S27_Rep1e_4Gy_4h_X


title: ifg1_cadmium_rep3

city: Saskatoon

first: Cheng-Wei

last: Wu

state: SK

address: 52 Campus Drive

country: Canada

institute: University of Saskatchewan

data_processing:
HISAT2 v2.0.5 used for mapping to the C. elegans reference genome
FeatureCounts v1.5.0-p3 used for Quantification
rMATS v3.2.5 used for Alternative Splicing analysis
StringTie v1.3.3 used for novel gene prediction.
DESeq2 v1.20.0 used for differential expression analysis
Genome_build: wbcel235
Supplementary_files_format_and_content: tab-delimited text files include differential gene expression and alternative splicing for each file

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
Total RNA extracted using the RNAqueous Total RNA Isolation Kit
Standard Illumina protocols with oligo-dT beads

value: 300uM cadmium (24h)


title: ifg1_cadmium_rep2


title: S154_Rep1e_4Gy_4h_12C

value: 4 Gy carbon-ion


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_1


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_24


title: SOK6_Rep1e_4Gy_4h_12C


title: ifg1_cadmium_rep1


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_4


title: ifg1_control_rep2

value: control


title: ifg1_control_rep3


title: S131_Rep1e_4Gy_4h_12C


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_2

value: Primordial germ cells


title: S40_Rep1e_4Gy_4h_12C


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_5


title: ifg1_control_rep1


title: WPMY-1 cells treated with RWF (250μg/ml) rep2

city: nanjing

first: jiakuan

last: liu

address: 12 xuefu road, pukou district

institute: nanjing university

hyb_protocol: 1 ug total RNA of each samples was used as input into the procedure as recommended by protocol.(Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays)

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G

data_processing: The data were analyzed with Moderated T-test. The algorithm for generating data in matrix tables was RMA.

label: biotin

label_protocol: The 5.5μg cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin.

growth_protocol: BPH1 and WPMY-1 Cells were respectively maintained in RPMI1640 and DMEM supplemented with 10% FBS, 100 units/ml penicillin and 100 μg/ml streptomycin at 37 ℃ under 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: BPH1 and WPMY-1  cells were treated with vehicle or RWF (250μg/ml)  for 24 hours. Then, cells were washed with PBS and lysed with Trizol.

value: WPMY-1 cells

tag: source tissue

value: human prostate stroma

tag: cell type source

value: RWF (250μg/ml)


title: N2_cadmium_rep3

value: wildtype


title: WPMY-1 cells treated with RWF (250μg/ml) rep1


title: WPMY-1 cells treated with vehicle rep1

source_name: WPMY-1 cells treated with vehicle

value: vehicle


title: WPMY-1 cells treated with vehicle rep2


title: S27_Rep1e_4Gy_4h_12C

value: HPV-negative


title: BPH1 cells treated with RWF (250μg/ml) rep2

source_name: BPH1 cells treated with RWF (250μg/ml)

value: BPH1 cells

value: human prostate epithelium


title: BPH1 cells treated with RWF (250μg/ml) rep1


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_3

tag: cell type

tag: developmental stage

value: Eed -/-

value: Male


title: BPH1 cells treated with vehicle rep2

source_name: BPH1 cells treated with vehicle


title: N2_cadmium_rep2


title: BPH1 cells treated with vehicle rep1


title: S99_Rep1e_4Gy_4h_12C

tag: replicate


title: SOK6_Rep1e_0Gy_4h

tag: time

value: oral ketratinocytes


title: KO3

city: Yangzhou

first: Zhijie

last: Lin

address: 136 Jiangyang road

department: Department of Immunology

institute: Yangzhou University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: spleen

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

value: spleen

value: leukocyte

value: non


title: KO1


title: N2_control_rep2


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_7

tag: gender


title: WT3

value: wt


title: S154_Rep1e_0Gy_4h

tag: treatment irradiation

value: head and neck squamous cell carinoma (HNSCC)

tag: hpv-status

value: HPV-positive


title: N2_cadmium_rep1

value: 300uM cadmium (24h)


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_8

value: Primordial germ cells


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_6


title: KO2


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_12

value: wild type


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_9


title: N2_control_rep3

value: control

value: wildtype


title: S33_Rep1e_4Gy_4h_12C

value: 4 Gy carbon-ion

value: HPV-negative


title: S40_Rep1e_0Gy_4h


title: WT2


title: small RNA-seq Input NAc Cocaine Rep2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: small RNAs (20-60nt)

data_processing:
csRNA-seq: Sequencing reads were trimmed for 3’ adapter sequences using HOMER (“homerTools trim −3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”) and aligned to the rat mRatBN7.2/rn7 genome assembly using STAR (Dobin et al., 2013) with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. Furthermore, reads with spliced or soft clipped alignments were discarded (the latter often removes erroneous alignments from abundant snRNA species). Transcription Start Regions (TSRs), representing 150 bp sized loci with significant transcription initiation activity (i.e. ‘peaks’ in csRNA-seq), were defined using HOMER’s findPeaks tool using the ‘-style tss’ option, which uses short input RNA-seq to eliminate loci with csRNA-seq signal arising from non-initiating, high abundance RNAs that nonetheless are captured and sequenced by the method (full description is available in Duttke et al. (Duttke et al., 2019)). To lessen the impact of outlier samples across the data collected for this study, csRNA-seq samples were first pooled into a single META-experiment per brain tissue region to collectively identify TSRs in each tissue.
Hi-C: Sequencing reads were first trimmed for sequences downstream of the restriction/ligation site (“GATCGATC”) and aligned to the rat genome using STAR with default parameters. Normalized interaction contact maps were then generated using HOMER. Juicer_tools was then used to generate the hic file.
snATAC-seq: Sequencing reads were processed using Cell Ranger ATAC 2.0 with a custom reference for Rattus norvegicus, built from the Ensembl Rnor 6.0 release 103 genome and annotation. The filtered results were subsequently analyzed using Signac 1.4.0 (Stuart et al., 2021).
Genome_build: rn7 (csRNA-seq, Hi-C), rn6 (snATAC-seq)
Supplementary_files_format_and_content: BED (genomic locations of transcription start regions - TSRs), H5 (compressed sparse matrix file), TSV (tab delimited), CSV (comma separated file), hic (chromatin contact binary file)

organism: Rattus norvegicus

source_name: small RNAs from NAc Cocaine Rep2

growth_protocol: Male Heterogenous Stock (HS) rats were trained to self-administer drugs in short access conditions (2 h/day for 4 days for oxycodone or 2 h/day for 10 days for cocaine) followed by long access conditions (12 h/day for oxycodone and 6 h /day for cocaine) for 14 days to develop escalation of drug intake. Age-matched naive male rats that were not exposed to any drug were used as control. Lastly, brain punches of PFC and NAc tissues were collected after 5 weeks of abstinence.

extract_protocol:
Brain punches of PFC and NAc tissues were extracted and snap-frozen (at -30°C). Cryosections of approximately 500 microns were used to dissect PFC and NAc punches on a –20°C frozen stage. Total RNA was extracted using the TRIZOL protocol.
csRNA-seq: csRNA-seq was performed as described previously (Duttke et al., 2019). Briefly, small RNAs of 15–60 nt were size selected from 0.3–1.0 microgram of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside, and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by Terminator 5’-phosphate-dependent exonuclease (Lucigen). Subsequent 5’ dephosphorylation by quickCIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’ adapter ligation by T4 RNA ligase 1 (NEB)(Hetzel et al., 2016). Thermostable quickCIP was used instead of rSAP and hence the bead clean-up step was skipped before heat denaturation prior to the second round of CIP treatment. The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) prior 3’ repair to select against degraded RNA fragments. Following cDNA synthesis, libraries were amplified for 11–14 cycles and sequenced SE75 on the Illumina NextSeq 500 sequencer.   Hi-C: PFC tissue as pulverized in liquid nitrogen. The Arima-Hi-C kit was used to construct the Hi-C libraries (#A410231, Arima Genomics). Sequencing of the libraries was conducted on an Illumina Novaseq S4 instrument.   snATAC-seq: Nuclei were isolated from brain tissue as previously described (Corces et al., 2018). Briefly, frozen tissue was homogenized using a 2 ml glass dounce with 1 ml cold 1x Homogenization Buffer (HB). Cell suspension was filtered using a 70 µm Flowmi strainer (BAH136800070, Millipore Sigma) and centrifuged at 350g for 5 min at 4°C. Nuclei were isolated by iodixanol (D1556, Millipore Sigma) density gradient. The nuclei iodixanol solution (25%) was layered on top of 40% and 30% iodixanol solutions. Samples were centrifuged in a swinging bucket centrifuge at 3,000g for 20 min at 4°C. Nuclei were isolated from the 30%-40% interface. Library preparation targeting the capture of ~6000 nuclei was carried out as detailed in the Chromium Next GEM Single Cell ATAC v1.1 manual (10x Genomics). Library sequencing was performed using the Illumina NovaSeq.

value: heterogeneous stock (HS)

value: prolonged abstinence after cocaine intravenous self-administration

value: nucleus accumbens (NAc)


title: S131_Rep1e_0Gy_4h


title: Liver_AktFoxo1TKO_refed_2h

city: Philadelphia

first: Paul

last: Titchenell

state: Pennsylvania

address: 3400 Civic Center Blvd.

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

data_processing:
Library strategy: GRO-seq
GRO-seq libraries were sequenced twice for better coverage, and sequencing replicates were pooled for each condition. Before alignment, sequencing reads were cleaned by trimming off low quality base, adapter and tailing poly-A sequences using cutadapt16. Trimmed reads of at least 25bp were selected and aligned to UCSC mm9 using bowtie with an option ‘--best --strata -m 1 -v 3’. Aligned reads within extremely high signal regions such as rRNA, snoRNA, snRNA and tRNA were removed before downstream analysis to minimize read-depth bias. To visualize transcriptional activity in genome browser, bigwig files were generated for (+) and (−) strands separately, where all the reads were extended to 150bp for smooth profile and (−) strand signal were presented as negative values.
Genome_build: mm9
Supplementary_files_format_and_content: Read-per-million (RPM) normalized stack-height profile in bigWig format

molecule: nuclear RNA

source_name: Liver

extract_protocol:
Nuclear Run-On (NRO): Nuclei were mixed with an equal volume of run-on buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 200 U/ml Superase-In, 1% Sarkosyl, 500 μM ATP, GTP and Br-UTP, 2 μM CTP) and incubated for 5 min at 30°C. Nuclear RNA was extracted with Trizol (Invitrogen) and treated with DNase (Ambion). RNA was hydrolyzed using fragmentation reagents (Ambion) for 13 min at 70°C and purified through a Micro Bio-Spin Column P-30 (Bio-Rad). RNA was treated with T4 polynucleotide kinase (New England Biolabs) for 1h at 37°C, then with an additional T4 polynucleotide kinase for 1h more, and inactivated for 5 min at 75°C. NRO-RNA immuno-precipitation: Anti-BrdU agarose beads (Santa Cruz) were rotated for 1h in blocking buffer (0.25x SSPE, 38 mM NaCl, 1 mM EDTA, 0.05% Tween-20, 0.1% PVP, and 0.1% BSA). Then NRO-RNA was rotated with beads for 1h, followed by washes twice in binding buffer (0.25x SSPE, 38 mM NaCl, 1 mM EDTA, 0.05% Tween-20), twice in low salt buffer (0.2x SSPE, 1 mM EDTA, 0.05% Tween-20), once in high salt buffer (0.2x SSPE, 1 mM EDTA, 0.05% Tween-20, 138 mM NaCl), and twice in TET buffer (TE pH 7.4, 0.05% Tween-20). BrdU-labeled RNA was eluted from the beads four times for 10 min with 100 μl elution buffer pre-heated to 42°C. RNA was precipitated by adding 300 mM NaCl, 1 µl of glycogen and 2.5 volumes of ethanol and incubated overnight at -20°C. RNA was resuspended in water (with 1 U/µl Superase-In and 0.05% Tween-20), denatured for 3 min at 65°C, and treated with poly(A)-polymerase (New England Biolabs) for 30 min at 37°C.
Library construction was performed as previously described (Core et al., 2008; Step, 2014; Wang et al., 2011). Synthesis of cDNA from RNA was performed as described previously (Wang et al., 2011). cDNA was denatured at 70°C for 3 min then products from 105-400 nucleotides size were excised and eluted from shredded gel pieces for 4h in TE + 0.1% Tween and precipitated by adding 1 µl of glycogen, 300 mM NaCl and 2 volumes of ethanol and incubated overnight at -20°C. cDNA was resuspended into circularization reaction and circularized with CircLigase (Epicentre) for 1 hour at 60°C, denatured for 10 min at 80°C, and relinearized by adding relinearization mix (25 mM KCl, 500 µM DTT) and APE I (15U; New England Biolabs). Linearized DNA was amplified by PCR using Phusion Hot Start II Kit. The PCR product from 150-305 nucleotides size were eluted from shredded gel pieces and purified using ChIP DNA Clean and Concentrator Kit (Genesee Scientific).

treatment_protocol: overnight fast or overnight fast followed by 2 hr. ad libitum chow refeeding

value: Liver

tag: model

tag: feeding condition

value: 2hr. Refed


title: Liver_AktDKO_refed_2h

value: AktDKO


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_14

source_name: Primordial germ cells

value: Male


title: WT1

value: spleen

tag: cell line

value: leukocyte

value: wt

value: non


title: small RNA-seq Input NAc Naive Rep2

description: small RNAs (20-60nt)

source_name: small RNAs from NAc Naive Rep2

tag: treatment

value: Naïve control


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_13

value: Primordial germ cells

tag: strain

value: wild type


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_10


title: N2_control_rep1

value: control

value: wildtype


title: SOK6_Rep1l_8Gy_72h_X

source_name: OKF6 cell line

value: 8 Gy X-ray

tag: tissue

value: oral ketratinocytes

value: HPV-negative


title: S99_Rep1e_0Gy_4h

value: head and neck squamous cell carinoma (HNSCC)


title: small RNA-seq Input NAc Naive Rep1

description: small RNAs (20-60nt)

source_name: small RNAs from NAc Naive Rep1

value: heterogeneous stock (HS)

value: nucleus accumbens (NAc)


title: small RNA-seq Input NAc Cocaine Rep1

description: small RNAs (20-60nt)

source_name: small RNAs from NAc Cocaine Rep1

value: prolonged abstinence after cocaine intravenous self-administration


title: S33_Rep1e_0Gy_4h


title: small RNA-seq Input NAc Oxycodone Rep1

description: small RNAs (20-60nt)

source_name: small RNAs from NAc Oxycodone Rep1

value: prolonged abstinence after oxycodone intravenous self-administration


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_11

value: Male


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_15


title: Liver_AktFoxo1WT_refed_2h

value: Liver

value: Control

value: 2hr. Refed


title: Liver_AktFoxo1WT_fasted

value: Overnight Fasted


title: small RNA-seq Input PFC Cocaine Rep2

description: small RNAs (20-60nt)

source_name: small RNAs from PFC Cocaine Rep2

value: prefrontal cortex (PFC)


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_17

value: Primordial germ cells

value: wild type


title: S27_Rep1e_0Gy_4h


title: Liver_AktWT_refed_2h


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_16


title: S40_Rep1l_8Gy_72h_X

source_name: UPCI:SCC040 cell line


title: S131_Rep1l_8Gy_72h_X

source_name: UPCI:SCC131 cell line


title: S154_Rep1l_8Gy_72h_X

source_name: UPCI:SCC154 cell line

value: HPV-positive


title: RNA-seq_E13.5_XY_ECKO_Rep_2

extract_protocol:
Male and female E11.5 and male E13.5 gonads were extracted and digested in 0.05% trypsin. GFP positive mPGCs were sorted into 300 µL RLT buffer and RNA extracted using the Rneasy Micro Kit (Qiagen)
Following cleanup, the samples were converted to cDNA following the Ovation RNA-seq System V2 protocol (Nugen). cDNA was indexed using the Ovation Rapid DR Multiplex System (Nugen).

value: Eed -/-


title: small RNA-seq Input PFC Cocaine Rep1

description: small RNAs (20-60nt)

source_name: small RNAs from PFC Cocaine Rep1


title: S33_Rep1l_8Gy_72h_X

source_name: Cal33 cell line

value: 8 Gy X-ray


title: S99_Rep1l_8Gy_72h_X

source_name: UPCI:SCC099 cell line

value: HPV-negative


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_20


title: RNA-seq_E13.5_XY_ECKO_Rep_3


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_21


title: RNA-seq_E13.5_XY_Control_Rep_4


title: small RNA-seq Input PFC Oxycodone Rep1

description: small RNAs (20-60nt)

source_name: small RNAs from PFC Oxycodone Rep1


title: small RNA-seq Input PFC Naïve Rep2

description: small RNAs (20-60nt)

source_name: small RNAs from PFC Naïve Rep2

value: Naïve control


title: Liver_AktWT_fasted


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_19


title: csRNA-seq NAc Cocaine Rep2

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from NAc Cocaine Rep2

value: heterogeneous stock (HS)


title: S154_Rep1l_8Gy_48h_X

value: head and neck squamous cell carinoma (HNSCC)


title: small RNA-seq Input PFC Oxycodone Rep2

description: small RNAs (20-60nt)

source_name: small RNAs from PFC Oxycodone Rep2


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_23

source_name: Primordial germ cells


title: RNA-seq_E13.5_XY_ECKO_Rep_1


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_18


title: S131_Rep1l_8Gy_48h_X


title: RNA-seq_E13.5_XY_Control_Rep_3


title: RNA-seq_E13.5_XY_Control_Rep_2


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_24


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_1


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_22


title: SOK6_Rep1l_8Gy_48h_X

value: oral ketratinocytes


title: csRNA-seq NAc Cocaine Rep1

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from NAc Cocaine Rep1

value: prolonged abstinence after cocaine intravenous self-administration

value: nucleus accumbens (NAc)


title: S27_Rep1l_8Gy_72h_X

source_name: Cal27 cell line


title: small RNA-seq Input PFC Naïve Rep1

description: small RNAs (20-60nt)

source_name: small RNAs from PFC Naïve Rep1


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_2

value: Male


title: S99_Rep1l_8Gy_48h


title: S27_Rep1l_8Gy_48h_X


title: SOK6_Rep1l_4Gy_72h_X

source_name: OKF6 cell line

value: 4 Gy X-ray


title: HG+HSP70-3

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

country: South Korea

institute: Inha university hospital

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 mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: mouse corpus cavernous tissue

growth_protocol: Growth in complement medium 199 (M199) contained with 20% fetal bovine serum (FBS), 1% penicillin/streptomycin, 0.5 mg/ml heparin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

treatment_protocol: Treatment with glucose for 5 days

tag: cell

value: mouse cavernous endothelial cells

value: high glucose+Hsp70


title: HG+HSP70-1


title: S33_Rep1l_8Gy_48h_X


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_5

tag: genotype


title: RNA-seq_E13.5_XY_Control_Rep_1


title: S40_Rep1l_8Gy_48h_X


title: HG+HSP70-4


title: csRNA-seq PFC Cocaine Rep2

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from PFC Cocaine Rep2

value: prefrontal cortex (PFC)


title: HG+HSP70-2


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_4

value: Primordial germ cells


title: HG 4

value: high glucose


title: csRNA-seq NAc Naive Rep2

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from NAc Naive Rep2


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_3

value: wild type


title: S154_Rep1l_4Gy_72h_X

value: HPV-positive


title: csRNA-seq NAc Oxycodone Rep1

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from NAc Oxycodone Rep1

value: prolonged abstinence after oxycodone intravenous self-administration


title: csRNA-seq NAc Naive Rep1

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from NAc Naive Rep1


title: csRNA-seq PFC Oxycodone Rep2

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from PFC Oxycodone Rep2


title: S99_Rep1l_4Gy_72h_X

value: HPV-negative


title: HG 2


title: S131_Rep1l_4Gy_72h_X

source_name: UPCI:SCC131 cell line


title: HG 1


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_7


title: csRNA-seq PFC Naïve Rep1

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from PFC Naïve Rep1

value: Naïve control


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_8


title: csRNA-seq PFC Cocaine Rep1

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from PFC Cocaine Rep1

value: heterogeneous stock (HS)


title: csRNA-seq PFC Naïve Rep2

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from PFC Naïve Rep2


title: csRNA-seq PFC Oxycodone Rep1

description: small capped RNAs (20-60nt)

source_name: Initiated transcripts from PFC Oxycodone Rep1


title: S40_Rep1l_4Gy_72h_X

source_name: UPCI:SCC040 cell line

value: head and neck squamous cell carinoma (HNSCC)


title: NG 3

value: normal glucose


title: S33_Rep1l_4Gy_72h_X

source_name: Cal33 cell line


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_17

source_name: Primordial germ cells


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_6


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_20


title: S27_Rep1l_4Gy_72h_X

source_name: Cal27 cell line


title: NG 2


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_18


title: CNL 16-0254 ORY1001 cDNA library

city: Portland

first: Sarah

middle: Ann

last: Carratt

state: Oregon

address: 3181 S.W. Sam Jackson Park Road, Mail Code KR-HEM

institute: OHSU

description: single cell CITE-seq

data_processing:
Sequencing from scRNAseq libraries was aligned using Cell Ranger
Expression matrices were processed using Seurat
Genome_build: hg38 or mm10

extract_protocol: 10X scRNAseq libraries were prepared using the NextGem 3' V3.0 kit according to the manufacturers instructions

value: CNL patient CD34+ cells

tag: time point

value: 24 hours

tag: antibody

value: TotalSeq A 0063 anti human CD45RA (biolegend 304157) Handle:TCAATCCTTCCGCTT  TotalSeq A 0064 anti human CD123 (biolegend 306037) Handle:CTTCACTCTGTCAGG  TotalSeq A 0062 anti human CD10 (biolegend 312231) Handle:CAGCCATTCATTAGG  TotalSeqA 0060 anti human CD90 (biolegend 328135) Handle:GCATTGTACGATTCA  TotalSeq A 0054 anti human CD34 (biolegend 343537) Handle:GCAGAAATCTCCCTT  TotalSeq A 0410 anti human CD38 (biolegend 356635) Handle:CCTATTCCGATTCCG  TotalSeqA0169 antihuman CD366/Tim-3(biolegend 345047) Handle:TGTCCTACCCAACTT  TotalSeqA0845 antihuman CD99 (biolegend 371317) Handle:ACCCGTCCCTAAGAA


title: NG 1


title: S154_Rep1l_4Gy_48h_X

source_name: UPCI:SCC154 cell line

value: 4 Gy X-ray


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_21

tag: cell type

value: Male


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 2) day 21

city: L'Hospitalet de Llobregat (Barcelona)

first: Jorge

last: Toledano

address: C/Feixa llarga s/n

country: Spain

institute: University of Barcelona

description:
test
SAMPLE 62

data_processing:
Target gene signals normalized to housekeeping genes; 2^∆∆Ct, where∆Ct = (Ct_Target − Ct_HKG)]. Normalized Template includes data of ∆Ct normalized to beta-actin and  Fold change workwheet reports data from  2^∆∆Ct comparing stimulated and unstimulated cells
Fold change workwheet reports data from  2^∆∆Ct comparing stimulated and unstimulated cells

label: SYBR Green

source_name: bone marrow

label_protocol: we quantified RNA using a microplate reader (Take3, Bio-Tek, Winooski, USA). Then, we retrotranscribed RNA into cDNA using the Transcriptor First Strand cDNA Synthesis kit (Roche, Basel, Switzerland) according to the recommendations of the manufacturer. We used qPCR to detect gene expression with the QuantiNova SYBR Green PCR Kit (Qiagen, Hilden, Germany): 10 ng of cDNA was amplified by an initial activation step of two minutes at 95°C, denaturation for 5 seconds at 95°C, and 40 cycles of hybridization/extension for 10 seconds at 60°C using the CFX96 Real-Time System (BioRad, Hercules, USA).

growth_protocol: The cell suspension culture was maintained at 3x105 cells/ml in RPMI 1640 medium (Sigma-Aldrich®, Sant Louis, USA) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich®, Sant Louis, USA) and 1% penicillin-streptomycin (Fisher Scientific, Hampton, USA). Cells were cultured in a humidity-controlled incubator at 37ºC with 5% CO2 supply. To enhance adhesion of the cells to the culture plates, we seeded them at a density of 3x104 cells/cm2 in the presence of phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich®, Sant Louis, USA) for 6 h. Then, the medium with PMA was removed, washed with DPBS, and the cells were exposed to the extracts previously obtained.

extract_protocol: RNA was isolated according to the recommendations of the manufacturer with the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany), which included DNase treatment

treatment_protocol: We separately sterilized IP debris (test) and Ti powder (control) with 96º ethanol and washed with DPBS. The required volume of cell culture medium was added in order to obtain a final concentration of 0.2 g of sample per ml of medium. Cell assays were performed by indirect culture with extracts according to section 8.2 of ISO 10993-5: after separation of metal particles and medium, we carried out the assays using this culture medium that had been previously exposed to metal particles.

value: primary human bone marrow mesenchymal stem cells

value: day 21


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 3) day 21

description:
test
SAMPLE 63


title: SOK6_Rep1l_4Gy_48h_X

source_name: OKF6 cell line

value: oral ketratinocytes


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 1) day 21

description:
test
SAMPLE 61


title: HG 3

source_name: mouse corpus cavernous tissue

value: mouse cavernous endothelial cells

value: high glucose


title: bone marrow Titanium + Osteo (rep 2) day 21

description:
test
SAMPLE 59


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_19

value: Primordial germ cells

tag: developmental stage

value: wild type


title: bone marrow Titanium + Osteo (rep 3) day 21

description:
test
SAMPLE 60


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_23


title: S131_Rep1l_4Gy_48h_X

tag: replicate

value: HPV-negative


title: CNL 16-0254 DMSO ADT library

description: single cell CITE-seq

value: DMSO


title: bone marrow Titanium + Osteo (rep 1) day 21

description:
test
SAMPLE 58

tag: time


title: CNL 16-0254 DMSO cDNA library

description: single cell CITE-seq


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_22

tag: gender


title: S40_Rep1l_4Gy_48h_X

tag: treatment irradiation


title: CNL 16-0254 ORY1001 ADT library

description: single cell CITE-seq


title: CD4 T Cells, Control rep5

city: Berkeley

first: David

last: DeTomaso

state: CA

address: Stanley Hall

department: Computational Biology

institute: UC Berkeley

data_processing:
Sequencing reads were initially filtered with Trimmomatic 0.32 to remove low quality ends and adapter sequences
Bowtie2 v2.2.9  was used to align reads to a reference transcriptome derived from the GRCm38 Mus musculus genome (NCBI Refseq).
RSEM 1.2.31 was used to compile the transcriptome and estimate transcript abundance following read alignment.
Prior to alignment, the GRCm38 reference was augmented to include the modified eGFP+IL23R functional knockout transcript.
Assembly: GRCm38
Supplementary files format and content: cd160_knockout_tpm.txt.gz: tab-delimited text table (genes x samples) of TPM-normalized gene expression values

source_name: CD4 T Cells

extract_protocol:
The intestinal CD4+ T cells were isolated from the colons of RAG1-/- recipients using a lamina propria dissociation kit (Miltenyi Biotec) as outlined in Pawlak M., DeTomaso, D. et al. 2021. Briefly, intestines were flushed with ice-cold buffer and opened longitudinally with scissors. The intraepithelial lymphocytes (IEL) were removed with buffer containing 1mM DTT. Lamina propria lymphocytes (LPL) were isolated from the intestinal mucosa by digestion at 37°C using a rotator. After digestion, the samples were homogenized using a gentleMACS (Miltenyi Biotec). CD4+ T cells were sorted into 5 μl TCL Buffer (QIAGEN) with 1% 2-mercaptoethanol, centrifuged and frozen at −80 °C.
For library construction, samples were thawed briefly at RT and ~20ul of each was transferred to a 96-well plate. The construction of the full-length RNA-seq libraries followed a modified SMART-Seq2 protocol (Picelli et al., 2013). After first strand cDNA synthesis and amplification, the cDNA was purified with a 0.7x single sided SPRI.  Each sample was normalized to 0.20ng/ul and then tagmented and indexed using the Nextera XT DNA library prep kit (Illumina). The individually barcoded libraries were then pooled and a final quality control was done on the BioAnalyzer (Agilent). The pool was normalized to 4nM, denatured using 0.2 N NaOh and 0.2 M Tris-HCL and diluted in HCL to prepare for sequencing. 1300ul of the final diluted pooled library was loaded for sequencing on a NextSeq 500/550. Paired end sequencing was performed using an Illumina 75 cycle Nextseq 500 high output V2 kit in accordance with Illumina protocol (Reads 38 cycles x2, Index 8 cycles x2).

treatment_protocol: For naive T cell adoptive transfer colitis, disease was induced by intraperitoneal injection of 4×105 naïve CD4+ T cells (CD4+CD25-CD45RBhigh) from CD160 knockout or wildtype littermate controls into Rag1-/- recipient mice. Disease progression was assessed by measurement of the body weight. At peak of disease, 5,000 CD4+ T cells were sorted from the colons directly into 5ul TCL buffer (containing b-mercaptoethanol according to the manufacturer's instructions, Qiagen) for bulk RNA-seq. cDNA libraries were prepared as outlined in Pawlak M., DeTomaso, D. et al. 2022 and sequenced.

value: Control


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_2

value: Female


title: bone marrow Osteo (rep 3) day 21

description:
control
SAMPLE 57


title: CD4 T Cells, Control rep3


title: S33_Rep1l_4Gy_48h_X

value: head and neck squamous cell carinoma (HNSCC)

tag: hpv-status


title: S99_Rep1l_4Gy_48h_X

source_name: UPCI:SCC099 cell line


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_4


title: scRNA-seq_E12-5_XY_Control_Embryo_2_Rep_24


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_1


title: CD4 T Cells, Control rep2


title: bone marrow Osteo (rep 2) day 21

description:
control
SAMPLE 56


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_3


title: S27_Rep1l_4Gy_48h_X


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 1) day 14

description:
test
SAMPLE 52

value: day 14


title: CD4 T Cells, CD160 Knockout rep4

value: CD160 Knockout


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 3) day 14

description:
test
SAMPLE 54


title: SOK6_Rep1l_4Gy_72h_12C

value: 4 Gy carbon-ion


title: bone marrow Osteo (rep 1) day 21

description:
control
SAMPLE 55


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_7


title: S154_Rep1l_4Gy_72h_12C

value: HPV-positive


title: bone marrow Titanium + Osteo (rep 2) day 14

description:
test
SAMPLE 50


title: S33_Rep1l_4Gy_72h_12C


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_5


title: CD4 T Cells, CD160 Knockout rep1


title: S99_Rep1l_4Gy_72h_12C


title: bone marrow Titanium + Osteo (rep 3) day 14

description:
test
SAMPLE 51


title: bone marrow Titanium + Osteo (rep 1) day 14

description:
test
SAMPLE 49


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_8


title: CD4 T Cells, Control rep1


title: CD4 T Cells, Control rep4


title: S131_Rep1l_4Gy_72h_12C


title: bone marrow Osteo (rep 2) day 14

description:
control
SAMPLE 47


title: bone marrow Osteo (rep 1) day 14

description:
control
SAMPLE 46


title: CD4 T Cells, CD160 Knockout rep2


title: CD4 T Cells cultured with TGFb+IL-6, GFPneg rep3

data_processing:
Sequencing reads were initially filtered with Trimmomatic 0.32 to remove low quality ends and adapter sequences
Bowtie2 v2.2.9  was used to align reads to a reference transcriptome derived from the GRCm38 Mus musculus genome (NCBI Refseq).
RSEM 1.2.31 was used to compile the transcriptome and estimate transcript abundance following read alignment.
Prior to alignment, the GRCm38 reference was augmented to include the modified eGFP+IL23R functional knockout transcript.
Assembly: GRCm38
Supplementary files format and content: cytokine_profiles_tpm.txt.gz: tab-delimited text table (genes x samples) of TPM-normalized gene expression values.  cytokine_profiles_sample_info.txt: tab-delimited table which contains GFP label and Cytokines, and stimulation for each sample.

extract_protocol:
Samples were collected into ~200ul of lysis buffer (TCL+BME) and stored in 1.5mL Eppendorf tubes. In preparation for library construction, samples were thawed briefly at RT and ~20ul of each was transferred to a 96-well plate.
The construction of the full-length RNA-seq libraries followed a modified SMART-Seq2 protocol (Picelli et al., 2013). After first strand cDNA synthesis and amplification, the cDNA was purified with a 0.7x single sided SPRI.  Each sample was normalized to 0.20ng/ul and then tagmented and indexed using the Nextera XT DNA library prep kit (Illumina). The individually barcoded libraries were then pooled and a final quality control was done on the BioAnalyzer (Agilent). The pool was normalized to 4nM, denatured using 0.2 N NaOh and 0.2 M Tris-HCL and diluted in HCL to prepare for sequencing. 1300ul of the final diluted pooled library was loaded for sequencing on a NextSeq 500/550. Paired end sequencing was performed using an Illumina 75 cycle Nextseq 500 high output V2 kit in accordance with Illumina protocol (Reads 38 cycles x2, Index 8 cycles x2).

treatment_protocol: A single-cell suspension was prepared from spleen and lymph nodes and red blood cells were removed by lysis with ACK buffer (Lonza). CD4+ T cells were enriched using microbeads (Miltenyi Biotec, Cat. #.: 130-117-043). Naïve CD4+ T cells (CD4+CD44lowCD62LhighCD25− ) were isolated by fluorescence-activated cell sorting (FACS) using a custom-built BD FACSAria instrument. Sorted naïve CD4+ T cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies (1mg/ml; BioXCell; Clone 145-2C11 and clone PV-1, respectively) in 96-well flat-bottom plates (50-100x103 cells/per well). Cells were cultured for 5 days with the following cytokine concentrations: IL-1b (20ng/ml); IL-6 (25ng/ml); IL-23 (20ng/ml); IL-12 (20ng/ml); IL-21 (20ng/ml); TGF-b (2ng/ml);  All recombinant cytokines were purchased from Biolegend (IL-21), R&D (IL-12, IL-1b, IL-6, IL-23) and Miltenyi Biotec (hTGF-b).

tag: cytokines

tag: gfp

value: GFPneg


title: CD4 T Cells, CD160 Knockout rep3


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 3) day 7

description:
test
SAMPLE 45

value: primary human bone marrow mesenchymal stem cells

value: day 7


title: bone marrow Osteo (rep 3) day 14

description:
control
SAMPLE 48


title: S40_Rep1l_4Gy_72h_12C


title: S131_Rep1l_4Gy_48h_12C


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_6


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 2) day 14

description:
test
SAMPLE 53


title: S27_Rep1l_4Gy_72h_12C


title: SOK6_Rep1l_4Gy_48h_12C

value: oral ketratinocytes


title: CD4 T Cells cultured with IL-1b+IL-6+IL-23, GFPneg rep3


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_9


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_13


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_10


title: CD4 T Cells cultured with IL-1b+IL-6+IL-23, GFPpos rep3

value: GFPpos


title: CD4 T Cells cultured with IL-12+IL-21, GFPneg rep3


title: S154_Rep1l_4Gy_48h_12C


title: CD4 T Cells cultured with TGFb+IL-6, GFPpos rep3


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_14


title: S27_Rep1l_4Gy_48h_12C


title: CD4 T Cells cultured with IL-12+IL-21, GFPpos rep3


title: S40_Rep1l_4Gy_48h_12C


title: CD4 T Cells cultured with IL-12+IL-21, GFPneg rep2


title: bone marrow Titanium + Osteo (rep 1) day 7

description:
test
SAMPLE 40


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 2) day 7

description:
test
SAMPLE 44


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 1) day 7

description:
test
SAMPLE 43


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_11


title: S99_Rep1l_4Gy_48h_12C


title: S33_Rep1l_4Gy_48h_12C


title: CD4 T Cells cultured with IL-12, GFPneg rep3


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_12

value: Eed -/-

value: Male


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_12

value: Primordial germ cells

value: wild type


title: S131_Rep1l_0Gy_72h

value: HPV-negative


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_15


title: bone marrow Titanium + Osteo (rep 3) day 7

description:
test
SAMPLE 42


title: bone marrow Titanium + Osteo (rep 2) day 7

description:
test
SAMPLE 41


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_10


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_16


title: S99_Rep1l_0Gy_72h


title: bone marrow Osteo (rep 3) day 7

description:
control
SAMPLE 39


title: SOK6_Rep1l_0Gy_72h


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_13


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 3) day 3

description:
test
SAMPLE 36

value: day 3


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_9


title: bone marrow Osteo (rep 1) day 7

description:
control
SAMPLE 37


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_14


title: bone marrow Titanium + Osteo (rep 3) day 3

description:
test
SAMPLE 33


title: bone marrow Osteo (rep 2) day 7

description:
control
SAMPLE 38


title: CD4 T Cells cultured with IL-12+IL-21, GFPneg rep1


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 2) day 3

description:
test
SAMPLE 35


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_15


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_11


title: S33_Rep1l_0Gy_72h


title: S40_Rep1l_0Gy_72h


title: bone marrow Titanium alloy (Ti6Al4V) + Osteo (rep 1) day 3

description:
test
SAMPLE 34


title: S154_Rep1l_0Gy_48h


title: CD4 T Cells cultured with TGFb+IL-6, GFPpos rep1


title: S27_Rep1l_0Gy_72h


title: bone marrow Titanium + Osteo (rep 2) day 3

description:
test
SAMPLE 32


title: CD4 T Cells cultured with TGFb+IL-6, GFPneg rep2


title: SOK6_Rep1l_0Gy_48h


title: S131_Rep1l_0Gy_48h


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_9

value: Female


title: CD4 T Cells cultured with TGFb+IL-6, GFPpos rep2


title: CD4 T Cells cultured with TGFb+IL-6, GFPneg rep1


title: CD4 T Cells cultured with IL-12+IL-21, GFPpos rep2


title: CD4 T Cells cultured with IL-1b+IL-6+IL-23, GFPneg rep2


title: S99_Rep1l_0Gy_48h

value: head and neck squamous cell carinoma (HNSCC)


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_16


title: S40_Rep1l_0Gy_48h


title: CD4 T Cells cultured with IL-1b+IL-6+IL-23, GFPpos rep1


title: CD4 T Cells cultured with IL-12, GFPneg rep2


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_10


title: CD4 T Cells cultured with IL-12+IL-21, GFPpos rep1


title: S33_Rep1l_0Gy_48h


title: 24DOXneg_IgG replicate 2

description: CUT&Tag

library_source: genomic

data_processing:
Sequencing from CUT&Tag was aligned using Bowtie2
Peaks were called using gopeaks
CPM normalized bigwigs merged with UCSC bigWigMerge
Bedgraphs coverted to bigwigs with UCSC bedGraphToBigWig
Differential enrichment was assessed using DESeq2
Genome_build: hg38 or mm10

molecule: genomic DNA

source_name: CSF3RT618I+SETBP1D868N-dox cell line

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2019

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1

value: doxycycline withdrawn, SETBP1 silenced

value: 24 hours

value: IgG (CST, cat 2729, lot 9)


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_15

extract_protocol:
Female E12.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific).
Single Cell RNA sequencing libraries were prepared according to the Smart Seq 2 single cell sequencing protocol (Picelli et al., 2014). The RNA was converted to cDNA in each well using Superscript II (Invitrogen). The cDNA was amplified in each well using a KAPA HiFI HotStart polymerase (KAPA Biosystems) in a PCR run for 18 cycles. cDNA was tagged via the Nextera Tagmentation kit (Illumina) using libraries A and C (Illumina). Indexed cDNA was pooled and run on a 2% agarose gel and the smear between 200-500 bp was extracted. Gel extract was cleaned with the Qiagen Gel Extraction Kit (Qiagen) and sent for sequencing.


title: bone marrow Osteo (rep 3) day 3

description:
control
SAMPLE 30


title: S154_Rep1l_0Gy_72h

extract_protocol:
Total RNA was extracted using Nucleospn RNA extraction kit from Macherey & Nagel
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HPV-positive


title: CD4 T Cells cultured with IL-1b+IL-6+IL-23, GFPneg rep1

value: GFPneg


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_12


title: bone marrow Osteo (rep 1) day 3

description:
control
SAMPLE 28

value: primary human bone marrow mesenchymal stem cells


title: CD4 T Cells cultured with IL-12, GFPneg rep1


title: bone marrow Titanium + Osteo (rep 1) day 3

description:
test
SAMPLE 31


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_14


title: S2_Rep1e_4Gy_4h_X

source_name: UD-SCC2 cell line

value: 4 Gy X-ray


title: CD4 T Cells cultured with IL-1b+IL-6+IL-23, GFPpos rep2

value: GFPpos


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_13

value: Eed -/-


title: 24DOXneg_H3K4me1 replicate 2

description: CUT&Tag

value: H3K4me1 (CST, cat 5326, lot 3)


title: Cell line from peripheral blood Titanium alloy (Ti6Al4V) (rep 3) 48h

description:
test
SAMPLE 24

source_name: Cell line from peripheral blood

tag: cell line

value: THP-1 acute monocytic leukemia cell line


title: S2_Rep1e_4Gy_4h_12C

value: 4 Gy carbon-ion


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_11

value: Primordial germ cells


title: S2_Rep1e_0Gy_4h


title: S27_Rep1l_0Gy_48h

value: HPV-negative


title: bone marrow d0 (rep 1) day 0

description:
control
SAMPLE 25

value: day 0


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_1

value: Female


title: bone marrow Osteo (rep 2) day 3

description:
control
SAMPLE 29

value: day 3


title: S2_Rep1l_8Gy_72h_X

value: 8 Gy X-ray

value: head and neck squamous cell carinoma (HNSCC)


title: 24DOXneg_H3K4me3 replicate 1

description: CUT&Tag

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1

tag: treatment

value: doxycycline withdrawn, SETBP1 silenced

value: 24 hours

value: H3K4me3 (CST, cat 9751, lot 10)


title: Cell line from peripheral blood Titanium alloy (Ti6Al4V) (rep 1) 48h

description:
test
SAMPLE 22


title: Cell line from peripheral blood Titanium (rep 3) 48h

description:
test
SAMPLE 21


title: bone marrow d0 (rep 3) day 0

description:
control
SAMPLE 27

value: primary human bone marrow mesenchymal stem cells


title: S2_Rep1e_8Gy_4h_X

value: HPV-positive


title: S2_Rep1l_4Gy_72h_X

value: 4 Gy X-ray


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_5

tag: strain

value: Eed -/-


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_16


title: 24DOXneg_H3K4me1 replicate 1

description: CUT&Tag

value: H3K4me1 (CST, cat 5326, lot 3)


title: Cell line from peripheral blood Titanium alloy (Ti6Al4V) (rep 2) 48h

description:
test
SAMPLE 23

value: THP-1 acute monocytic leukemia cell line


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_2

value: Primordial germ cells


title: Cell line from peripheral blood Titanium (rep 1) 48h

description:
test
SAMPLE 19


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_4


title: 24DOXneg_H3K27Ac replicate 2

description: CUT&Tag


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_7


title: bone marrow d0 (rep 2) day 0

description:
control
SAMPLE 26


title: S2_Rep1l_8Gy_48h_X

tag: tissue


title: 24DOXneg_H3K4me3 replicate 2

description: CUT&Tag


title: Cell line from peripheral blood Titanium (rep 2) 48h

description:
test
SAMPLE 20


title: 24DOXpos_H3K4me3 replicate 2

description: CUT&Tag

value: doxycycline present, SETBP1 expressed


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_3


title: 24DOXneg_IgG replicate 1

description: CUT&Tag

value: IgG (CST, cat 2729, lot 9)


title: 24DOXpos_H3K4me1 replicate 2

description: CUT&Tag


title: S2_Rep1l_4Gy_48h_12C

value: 4 Gy carbon-ion


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_9

value: wild type

value: Male


title: Cell line from peripheral blood LPS (rep 1) 48h

description:
test
SAMPLE 16


title: S2_Rep1l_0Gy_48h

value: head and neck squamous cell carinoma (HNSCC)


title: 24DOXneg_H3K27Ac replicate 1

description: CUT&Tag

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1


title: 24DOXpos_H3K27Ac replicate 2

description: CUT&Tag


title: Cell line from peripheral blood TCP (rep 3) 48h

description:
control
SAMPLE 15


title: S2_Rep1l_4Gy_48h_X


title: Cell line from peripheral blood LPS (rep 3) 48h

description:
test
SAMPLE 18


title: 24DOXpos_IgG replicate 2

description: CUT&Tag


title: Cell line from peripheral blood LPS (rep 2) 48h

description:
test
SAMPLE 17


title: S2_Rep1l_4Gy_72h_12C


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_6

value: Female


title: scRNA-seq_E12-5_XX_ECKO_Embryo_2_Rep_8


title: S2_Rep1l_0Gy_72h


title: Cell line from peripheral blood TCP (rep 1) 48h

description:
control
SAMPLE 13


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_12


title: Young CSF 6hr sample 4

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_6hr_4

data_processing:
Library strategy: SLAM-seq
Each experimental setup was processed as described below:
1. Raw sequencing files were demultiplexed with bcl2fastq, reads were aligned using STAR, and counts of technical replicates were summed up using DESeq2 before performing normalization and differential expression analysis with standard settings.
2. Sequencing quality control was performed using FastQC v0.11.8 and summary reports were generated with MultiQC v1.7. FASTQ files were then analyzed using the SLAM-DUNK pipeline v0.3.4 and the related alleyoop toolchain. The pipeline comprises 1) read mapping, 2) alignment filtering, 3) SNP calling and correction, and 4) 3'-UTR sequence counting. Using NextGenMap reads were aligned against the genome of Rattus norvegicus (release 6.0), which was downloaded in FASTA format from Ensembl release v97. For mapping the following parameters were set; '-5 12, -a 4, -n 1, -ss' leaving rest at default. Resulting Binary sequence Alignment/Map (BAM) format files were filtered to remove low-quality alignments using the parameters '-mq 2, -mi 0.95, -nm -1’ and rest at default. Next, SNPs in alignments, in particular the T to C (T>C) conversions, were called with parameters '-c 10, -f 0.8' and others remaining at default. Statistical independence of distributions of true SNP-callings identified by VarScan2 in relation to the number of T>C reads was assessed with a Mann-Whitney-U test for each sample as initially described in the alleyoop snpeval toolchain module. For the reference set of 3'-UTRs, a genome feature file (GFF3) for the Rattus norvegicus genome (release 6.0) was downloaded from Ensembl release v97, filtered to retain only three_prime_utr features and converted to Browser Extensible Data (BED) format using bedops v2.4.36. The BED file was used in combination with parameters '-c 1, -q 27' for the SLAMDUNK count command, leaving other parameters at default. Resulting 3'-UTR T>C and total read counts were added up on gene-level along all transcripts and alternative 3'-UTRs available per transcript. Entire down-stream analysis was performed using R v3.6.1, data.table v1.12.2, and common tidyverse packages (tidyr, dplyr, purrr, stringr, ggplot2). Differential gene expression analysis was carried out using DESeq2 v1.26.0 on the T>C count and total count matrices separately with standard settings with alpha level set to 0.05. In total, six DESeq2 experiments were performed, two with pooled timepoints (1hr + 6hr) per read-type (design variables Treatment and Time) and four with separate timepoint per read-type (design variable Treatment only). Effect size was calculated using the implementation of cohen’s d from the effsize v0.7.6 package. Gene set enrichment and over-representation analyses were performed using GeneTrail 3.0 65. Category source databases were adjusted independently, and P-values were corrected using the false discovery rate controlling procedure by Benjamini-Hochberg and considered significant if smaller than 0.05.
3. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
4. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
5. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
Genome_build: GRCm38, Rnor_6.0.97
Supplementary_files_format_and_content: For each sample raw gene counts are provided. For SLAM-seq samples also the raw T-to-C counts are provided.

source_name: Primary rat OPC culture

growth_protocol: OPCs were isolated  from P7-P8 Sprague-Dawley (Charles Rivers) rat brains by immunopanning and grown in serum-free defined medium, as previously described (Emery, B. & Dugas, J. C. Purification of oligodendrocyte lineage cells from mouse cortices by immunopanning. Cold Spring Harb Protoc 2013)

extract_protocol:
RNA extraction was done following anabolic kit protocol. All cell culture and RNA extraction steps were done in the dark under red-light following manufacturer’s recommendations.
Library preparation was done with QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (FWD) (015, Lexogen) with the indicated modifications to adjust to low-RNA input.
After normalization and pooling, libraries were sequenced on a Nextseq550 (Illumina) using single-end 75-bp reads. Libraries were sequenced to a mean depth of ~30 million reads per sample. Raw sequencing files were demultiplexed with bcl2fastq and resulting FASTQ files combined across lanes and per sample.

treatment_protocol: Optimal s4U concentration was assessed following SLAMseq 64 Explorer Kit – Cell Viability Titration Module (061, Lexogen) following manufacturer’s recommendations. In brief, OPCs were incubated with increasing doubling concentrations of s4U (1.95-2000mM) and viability was assessed with live-dead ratio as described above and with ATP incorporation following manufacturer’s recommendations (Promega,G7571). A final concentration of 62.5uM was found as the highest concentration without compromising on cell viability within 12 hrs (twice the duration of the intended experiment). SLAMseq experiment was conducted following SLAMseq Kinetics Kit - Anabolic Kinetics Module protocol (061, Lexogen). In brief, following initial growth of 4 days in 10cm dishes, 30,000 OPCs were plated in 315ml full proliferation medium on PDL-covered 24-well plates (one plate per timepoint) overnight. 35ml of pooled YH-CSF or aCSF spiked in with 625mM S4U (10x concentration) were added gently to minimize confounding induction of gene expression. One- or six-hours later the medium was removed and cells were scraped with 1ml Trizol (Thremo, 15596018), transferred to foil-covered tubes and frozen until RNA extraction.

tag: experiment batch

tag: experiment type

value: SLAM-seq

tag: age

tag: Sex

tag: experimental group

value: Treatment

tag: timepoint

tag: specimen

value: Young human CSF

value: OPC

tag: cell compartment

value: Whole cell


title: Cell line from peripheral blood TCP (rep 2) 48h

description:
control
SAMPLE 14

tag: time


title: 24DOXpos_H3K4me1 replicate 1

description: CUT&Tag

tag: cell type

tag: time point

value: 24 hours

tag: antibody


title: 24DOXpos_IgG replicate 1

description: CUT&Tag


title: Young CSF 6hr sample 3

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_6hr_3


title: Cell line from peripheral blood Titanium alloy (Ti6Al4V) (rep 3) 24h

description:
test
SAMPLE 12


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_10

data_processing:
The RNA-seq reads were aligned using HISAT2
Genes that are expressed (read counts > 0) in at least one replicate in both control and ECKO are included for analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR
WGBS reads were aligned with BS Seeker 2.  CG sites with read depth >= 4 are preserved in the Cgmap.gz file.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files includes RPKM values for each sample.

tag: developmental stage

tag: genotype

tag: gender


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_13

tag: strain


title: 24DOXpos_H3K4me3 replicate 1

description: CUT&Tag

tag: treatment

value: H3K4me3 (CST, cat 9751, lot 10)


title: Young CSF 6hr sample 2

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_6hr_2

tag: experiment batch


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_11


title: Cell line from peripheral blood Titanium alloy (Ti6Al4V) (rep 1) 24h

description:
test
SAMPLE 10

tag: cell line

value: THP-1 acute monocytic leukemia cell line


title: Young CSF 6hr sample 5

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_6hr_5

tag: experiment type

tag: age


title: Cell line from peripheral blood Titanium (rep 3) 24h

description:
test
SAMPLE 9


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_15

value: Primordial germ cells


title: Artificial CSF 6hr sample 5

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_6hr_5

tag: Sex

tag: experimental group

value: Control

value: Artificial CSF


title: Cell line from peripheral blood Titanium (rep 2) 24h

description:
test
SAMPLE 8


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_16


title: Artificial CSF 6hr sample 4

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_6hr_4

tag: timepoint

tag: specimen


title: mIMCD-3 Cilia-bPAC cells, treatment 47 h dark + 1 h light, experiment number e19115

city: Bonn

first: Jan

middle: N.

last: Hansen

address: Venusberg Campus 1

institute: University of Bonn

data_processing:
Sequencing data was demultiplexed and converted into fastq format using bcl2fastq2 v2.20
Kallisto version 0.44.0 was used to quantify abundances of transcripts from RNA-seq data.
Genome_build: Mus musculus, Release M16 (GRCm38.p5)
Supplementary_files_format_and_content: Count table (csv file) showing the pseudo-counts determined by kallisto. Rows reveal different transcripts, Columns reveal the different samples.

source_name: immortalized kidney cell line (mIMCD-3)

growth_protocol: mIMCD-3 (CRL-2123) WT cells were obtained and authenticated from American Type Culture Collection (ATCC). Cyto-bPAC cells were described in Hansen et al., eLife, 2020. Cilia-bPAC cells were generated as folllows: WT mIMCD-3 cells were transfected with pc3.1-mNPHP3(201)-bPAC-mCherry (Hansen et al., 2020) and selected with 1.2 mg/ml Geneticin™ (G418 Sulfate, Gibco, #11811031) until cell clones could be picked, analyzed, and maintained as monoclonal cell lines. All cells have been tested and are free from mycoplasma and other microorganisms. All cells were maintained in DMEM/F12 (1:1) medium, supplemented with GlutaMax (Gibco, #31331-028) and 10 % FCS at 37°C and 5 % CO2. For Cilia-bPAC and Cyto-bPAC cells, growth medium during maintenance was additionally supplemented with 0.8 mg/ml G418. During the experiment, no G418 was supplemented. For the experiment, cells were seeded in triplicates in 6-well plates (2.46 x 105 cells/well, Greiner CELLSTAR, #657160) and kept in the dark during the entire experiment (except for specific light stimulations in some conditions, see treatment column). 24 h after seeding, cells were starved (starvation medium: reduced growth medium with 0.5 % FCS).

extract_protocol:
Cell lysis was performed under dim red light only to prevent activation of bPAC: Cells were washed ones with PBS and next directly lysed from the plates by addition of 400 µl / well of Trizol (Thermo Fisher Scientific, #15596026). Triplicates were pooled into one tube. RNA was extracted using the miRNeasy micro kit (Qiagen). Total RNA quantity and quality were determined via RNA assay on a Tapestation 4200 system (Agilent).
5 ng total RNA were used as an input for NGS library preparation following the SMART-Seq2 protocol (Picelli et al., 2014). Final libraries were quantified by HS dsDNA assay on a Qubit (Invitrogen) and fragment size distribution was checked via D5000 assay on a Tapestation 4200 system (Agilent). Libraries were equimolarly pooled and clustered at 1.4 pM and sequenced SR 75 cycles on a NextSeq500 instrument with High Output v2 chemistry (Illumina) to ~10 million raw reads per sample.

treatment_protocol: Either 24 h or 47 h after starting the starvation, cells were stimulated for 1 h with light (465 nm, 38.8 µW/cm²), or, alternatively, they were kept in the dark during the entire time. WT cells in the dark were stimulated also with DMSO or 10 mM Forskolin for 1 h (see characteristics for individual samples).

tag: experimentid

value: Cilia-bPAC

value: immortalized kidney cell line (mIMCD-3)

value: 47 h dark + 1 h light


title: mIMCD-3 WT cells, treatment 48 h dark + DMSO (1:1000) during last hour, experiment number e19115

value: WT


title: 24DOXpos_H3K27Ac replicate 1

description: CUT&Tag

tag: cell type

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1

value: doxycycline present, SETBP1 expressed


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_10

value: Eed -/-

value: Female


title: Cell line from peripheral blood Titanium (rep 1) 24h

description:
test
SAMPLE 7

tag: time


title: Artificial CSF 6hr sample 2

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_6hr_2

value: SLAM-seq

value: Male

tag: cell compartment


title: mIMCD-3 Cilia-bPAC cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e19115

value: 24 h dark + 1 h light + 23 h dark


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_9

tag: developmental stage


title: Cell line from peripheral blood Titanium alloy (Ti6Al4V) (rep 2) 24h

description:
test
SAMPLE 11


title: Young CSF 6hr sample 1

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_6hr_1

value: Treatment

value: Young human CSF

value: OPC

value: Whole cell


title: mIMCD-3 Cilia-bPAC cells, treatment 48 h dark, experiment number e19115

tag: genotype

value: 48 h dark


title: Cell line from peripheral blood LPS (rep 3) 24h

description:
test
SAMPLE 6

value: THP-1 acute monocytic leukemia cell line


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_12

value: Primordial germ cells

tag: gender


title: Cell line from peripheral blood LPS (rep 2) 24h

description:
test
SAMPLE 5


title: Artificial CSF 6hr sample 1

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_6hr_1

value: Control

value: Artificial CSF


title: scRNA-seq_E12-5_XY_Control_Embryo_1_Rep_14

tag: strain

value: wild type


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_11


title: mIMCD-3 Cyto-bPAC cells, treatment 47 h dark + 1 h light, experiment number e19115

value: Cyto-bPAC

value: immortalized kidney cell line (mIMCD-3)

tag: treatment

value: 47 h dark + 1 h light


title: mIMCD-3 Cyto-bPAC cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e19115


title: Young CSF 1hr sample 5

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_1hr_5

tag: experiment batch


title: mIMCD-3 Cyto-bPAC cells, treatment 48 h dark, experiment number e19115

tag: cell line


title: Cell line from peripheral blood LPS (rep 1) 24h

description:
test
SAMPLE 4


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_13

value: Eed -/-

value: Female


title: Young CSF 1hr sample 4

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_1hr_4

tag: experiment type

value: SLAM-seq

value: Male


title: Artificial CSF 6hr sample 3

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_6hr_3

tag: age


title: Young CSF 1hr sample 3

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_1hr_3

tag: Sex

value: Treatment


title: mIMCD-3 WT cells, treatment 47 h dark + 1 h light, experiment number e19115

value: WT


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_15


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_14


title: Cell line from peripheral blood TCP (rep 2) 24h

description:
control
SAMPLE 2


title: mIMCD-3 WT cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e19115

value: 24 h dark + 1 h light + 23 h dark


title: Young CSF 1hr sample 2

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_1hr_2

tag: experimental group

value: Young human CSF

value: OPC

value: Whole cell


title: Cell line from peripheral blood TCP (rep 1) 24h

description:
control
SAMPLE 1

value: THP-1 acute monocytic leukemia cell line


title: mIMCD-3 WT cells, treatment 48 h dark, experiment number e19115

value: 48 h dark


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_16

value: Primordial germ cells


title: Young CSF 1hr sample 1

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
Young_CSF_1hr_1

tag: timepoint


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_18

value: wild type


title: Artificial CSF 1hr sample 4

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_1hr_5

value: Control

tag: specimen

value: Artificial CSF


title: mIMCD-3 WT cells, treatment 48 h dark + Forskolin 10 µM during last hour, experiment number e19103

tag: experimentid

value: immortalized kidney cell line (mIMCD-3)


title: ELDR over expressed (stable) [Exp A2]

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

description: exp_A2.TCGGAGACCT-AGTAGCTAGT.HFVJMDSXY_TCGGAGACCT-AGTAGCTAGT

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.24.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma.
Assembly: Ensembl release 76
Supplementary files format and content: gene raw counts

source_name: normal oral keratinocyte (NOK)

growth_protocol: Normal oral keratinocytes (NOK) cells (kindly gifted by Karl Mugner) were maintained in Keratinocyte SFM medium supplemented with EGF and bovine pituitary extract (GIBCO, Life technologies) and 1% penicillin/ streptomycin.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen,CA).
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq using standard Illumina protocols.

treatment_protocol: ELDR [NR_110426.1] pcDNA3.1 plasmid DNA or control plasmid DNA (1 µg) was transfected into NOK cell lines, selected with G418 (Sigma) and pooled for establishment of a stable cell line (NOK-ELDR).

value: NOK

tag: cell type

value: normal oral keratinocytes

value: ELDR over expressed


title: mIMCD-3 WT cells, treatment 48 h dark + DMSO (1:1000) during last hour, experiment number e19103


title: Cell line from peripheral blood TCP (rep 3) 24h

description:
control
SAMPLE 3

tag: time


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_17

value: Female


title: Artificial CSF 1hr sample 3

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_1hr_3

value: SLAM-seq

value: Male

tag: cell compartment


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_20

tag: developmental stage


title: ELDR over expressed (stable) [Exp A3]

description: exp_A3.AATGCGATGG-GCACACAGCA.HFVJMDSXY_AATGCGATGG-GCACACAGCA

tag: genotype


title: ELDR over expressed (stable) [Exp A1]

description: exp_A1.AACGCACGAG-ATAACCACAC.HFVJMDSXY_AACGCACGAG-ATAACCACAC


title: Artificial CSF 1hr sample 2

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_1hr_2


title: Control 3

description: control_3.CACCGAATCA-CTTAGTCCAA.HFVJMDSXY_CACCGAATCA-CTTAGTCCAA

value: WT (wild_type)


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_19

tag: gender


title: mIMCD-3 Cilia-bPAC cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e19103

value: Cilia-bPAC

value: 24 h dark + 1 h light + 23 h dark


title: Artificial CSF 1hr sample 1

description:
sample_to_Gene_expression_matrix_RawReadCounts.txt
sample_to_Gene_expression_matrix_RawTcReadCounts.txt
aCSF_1hr_1

value: OPC

value: Whole cell


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_21

tag: strain


title: Control 2

description: control_2.CCTCTATCTC-CTCATTCTGC.HFVJMDSXY_CCTCTATCTC-CTCATTCTGC

tag: treatment


title: mIMCD-3 Cilia-bPAC cells, treatment 48 h dark, experiment number e19103

value: 48 h dark


title: mIMCD-3 Cyto-bPAC cells, treatment 47 h dark + 1 h light, experiment number e19103

value: Cyto-bPAC

value: 47 h dark + 1 h light


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_23

value: Primordial germ cells

value: wild type


title: invitro_DART-seq-APO1 Replicate 3

city: Durham

first: Huanyu

last: Zhu

state: NC

address: 307 Research Drive

department: Biochemistry

institute: Duke University

description:
processed data file:
inVitro_APO1-DF2YTH-YTHmut.bed
inVitro_APO1-DF2_D422N-YTHmut.bed
inVitro_APO1-DF2YTH-YTHblock.bed
inVitro_APO1-DF2_D422N-YTHblock.bed

data_processing:
library strategy: DART-Seq (deamination adjacent to RNA modification targets)
Trimming of adaptor sequences (Flexbar 3.0.3)
Alignment to hg19 using NovoAlign
Deduplication using SAMtools
YTHmut or YTHblock samples: Bam files were mered using SAMtools
Identification of m6A sites usin Bullseye
Genome_build: hg19
Supplementary_files_format_and_content: Bed files are lists of m6A sites identified within each replicate using Bullseye. High confidence m6A sites in paper were a result of keeping only these sites that occur in at least 2 of 3 replicates.

source_name: Kidney

growth_protocol: HEK293T cells expressing DART or ADAR variants through transient transfection were cultured in DMEM + 10% FBS with penicillin/streptomycin.

extract_protocol:
Cellular DART-seq: Trizol was used to extract total RNA from cells expressing DART protein variants. The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 1000ng of input RNA. In vitro DART-seq: Trizol was used to extract total RNA from HEK293T cells. After in vitro DART treatment, edited RNA was isolated using RNeasy MiElute Cleanup Kit (Qiagen 74204).
Cellular DART-seq: The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 1µg of input RNA. In vitro DART-seq: The NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB, E6420) was used to enerate sequencin libraries using the full 50ng of total RNA used during in vitro DART incubation.

treatment_protocol: STM2457 treatment: When cells were ~40% confluent. HEK293T cells were treated with 10µM of STM2457 for 72hrs. After 48hrs, ADAR-YTH, ADAR-YTH_D422N, ADAR-YTHmut, or ADAR were transiently transfected into treated cells.

value: 4hr, 37C, 50ng RNA, 250ng APOBEC1


title: mIMCD-3 Cilia-bPAC cells, treatment 47 h dark + 1 h light, experiment number e19103

value: immortalized kidney cell line (mIMCD-3)


title: mIMCD-3 Cyto-bPAC cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e19103


title: mRNA-seq NAc Oxycodone Rep2

description: mRNA transcripts from NAc Oxycodone Rep2

data_processing:
csRNA-seq: Sequencing reads were trimmed for 3’ adapter sequences using HOMER (“homerTools trim −3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”) and aligned to the rat mRatBN7.2/rn7 genome assembly using STAR (Dobin et al., 2013) with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. Furthermore, reads with spliced or soft clipped alignments were discarded (the latter often removes erroneous alignments from abundant snRNA species). Transcription Start Regions (TSRs), representing 150 bp sized loci with significant transcription initiation activity (i.e. ‘peaks’ in csRNA-seq), were defined using HOMER’s findPeaks tool using the ‘-style tss’ option, which uses short input RNA-seq to eliminate loci with csRNA-seq signal arising from non-initiating, high abundance RNAs that nonetheless are captured and sequenced by the method (full description is available in Duttke et al. (Duttke et al., 2019)). To lessen the impact of outlier samples across the data collected for this study, csRNA-seq samples were first pooled into a single META-experiment per brain tissue region to collectively identify TSRs in each tissue.
Hi-C: Sequencing reads were first trimmed for sequences downstream of the restriction/ligation site (“GATCGATC”) and aligned to the rat genome using STAR with default parameters. Normalized interaction contact maps were then generated using HOMER. Juicer_tools was then used to generate the hic file.
snATAC-seq: Sequencing reads were processed using Cell Ranger ATAC 2.0 with a custom reference for Rattus norvegicus, built from the Ensembl Rnor 6.0 release 103 genome and annotation. The filtered results were subsequently analyzed using Signac 1.4.0 (Stuart et al., 2021).
RNA-seq: Sequencing reads were aligned to the rat mRatBN7.2/rn7 genome assembly using STAR (Dobin et al., 2013) with default parameters. Gene expression counts were calculated using featureCounts.
Assembly: rn7 (csRNA-seq, RNA-seq, Hi-C), rn6 (snATAC-seq)
Supplementary files format and content: BED (genomic locations of transcription start regions - TSRs), gene_counts.txt (tab-delimited text file with counts per gene from RNA-seq experiments), H5 (compressed sparse matrix file), TSV (tab delimited), CSV (comma separated file), hic (chromatin contact binary file)

source_name: nucleus accumbens (NAc)

extract_protocol:
Brain punches of PFC and NAc tissues were extracted and snap-frozen (at -30°C). Cryosections of approximately 500 microns were used to dissect PFC and NAc punches on a –20°C frozen stage. Total RNA was extracted using the TRIZOL protocol.
csRNA-seq: csRNA-seq was performed as described previously (Duttke et al., 2019). Briefly, small RNAs of 15–60 nt were size selected from 0.3–1.0 microgram of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside, and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by Terminator 5’-phosphate-dependent exonuclease (Lucigen). Subsequent 5’ dephosphorylation by quickCIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’ adapter ligation by T4 RNA ligase 1 (NEB)(Hetzel et al., 2016). Thermostable quickCIP was used instead of rSAP and hence the bead clean-up step was skipped before heat denaturation prior to the second round of CIP treatment. The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) prior 3’ repair to select against degraded RNA fragments. Following cDNA synthesis, libraries were amplified for 11–14 cycles and sequenced SE75 on the Illumina NextSeq 500 sequencer.   RNA-seq: RNA sequencing libraries were generated using the Illumina Stranded mRNA Prep (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End reads (PE100) to a depth of approximately 25 million reads per sample on an Illumina NovaSeq 6000.  Hi-C: PFC tissue as pulverized in liquid nitrogen. The Arima-Hi-C kit was used to construct the Hi-C libraries (#A410231, Arima Genomics). Sequencing of the libraries was conducted on an Illumina Novaseq S4 instrument.   snATAC-seq: Nuclei were isolated from brain tissue as previously described (Corces et al., 2018). Briefly, frozen tissue was homogenized using a 2 ml glass dounce with 1 ml cold 1x Homogenization Buffer (HB). Cell suspension was filtered using a 70 µm Flowmi strainer (BAH136800070, Millipore Sigma) and centrifuged at 350g for 5 min at 4°C. Nuclei were isolated by iodixanol (D1556, Millipore Sigma) density gradient. The nuclei iodixanol solution (25%) was layered on top of 40% and 30% iodixanol solutions. Samples were centrifuged in a swinging bucket centrifuge at 3,000g for 20 min at 4°C. Nuclei were isolated from the 30%-40% interface. Library preparation targeting the capture of ~6000 nuclei was carried out as detailed in the Chromium Next GEM Single Cell ATAC v1.1 manual (10x Genomics). Library sequencing was performed using the Illumina NovaSeq.

value: heterogeneous stock (HS)

value: prolonged abstinence after oxycodone intravenous self-administration

tag: tissue

value: nucleus accumbens (NAc)


title: mIMCD-3 Cyto-bPAC cells, treatment 48 h dark, experiment number e19103

tag: cell line


title: mRNA-seq NAc Oxycodone Rep1

description: mRNA transcripts from NAc Oxycodone Rep1


title: invitro_DART-seq-YTH-block Replicate 3

description:
processed data file:
inVitro_APO1-DF2YTH-YTHblock.bed
inVitro_APO1-DF2_D422N-YTHblock.bed

value: 1ug of YTH is incubed with 50ng of RNA for 1hr, prior to 4hr, 37C incubation with 250ng of APOBEC1-YTH-D422N


title: mIMCD-3 WT cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e19103

value: WT


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_22

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

institute: Academia Sinica

value: Female


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_24


title: mIMCD-3 WT cells, treatment 47 h dark + 1 h light, experiment number e19103


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_1

value: Eed -/-

value: Male


title: invitro_DART-seq-APO1 Replicate 1


title: Control 1

description: control_1.CCTCCAGGTA-ATTCACGTGA.HFVJMDSXY_CCTCCAGGTA-ATTCACGTGA

value: NOK

value: normal oral keratinocytes

value: WT (wild_type)

value: Control


title: invitro_DART-seq-APO1 Replicate 2


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_4


title: mRNA-seq NAc Cocaine Rep2

description: mRNA transcripts from NAc Cocaine Rep2

value: prolonged abstinence after cocaine intravenous self-administration


title: invitro_DART-seq-YTH-block Replicate 1


title: mRNA-seq NAc Naive Rep1

description: mRNA transcripts from NAc Naive Rep1

value: Naïve control


title: invitro_DART-seq-YTH-block Replicate 2


title: mRNA-seq NAc Cocaine Rep1

description: mRNA transcripts from NAc Cocaine Rep1


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_5

value: Primordial germ cells


title: mRNA-seq PFC Cocaine Rep1

description: mRNA transcripts from PFC Cocaine Rep1

source_name: prefrontal cortex (PFC)

value: prefrontal cortex (PFC)


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_2

source_name: Primordial germ cells


title: mRNA-seq NAc Naive Rep2

description: mRNA transcripts from NAc Naive Rep2


title: mIMCD-3 Cilia-bPAC cells, treatment 47 h dark + 1 h light, experiment number e1994

value: Cilia-bPAC

value: immortalized kidney cell line (mIMCD-3)

value: 47 h dark + 1 h light


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_3


title: mRNA-seq PFC Oxycodone Rep2

description: mRNA transcripts from PFC Oxycodone Rep2

value: heterogeneous stock (HS)

value: prolonged abstinence after oxycodone intravenous self-administration


title: invitro_DART-seq-APOBEC1-YTHmut Replicate 3

description:
processed data file:
inVitro_APO1-DF2YTH-YTHmut.bed
inVitro_APO1-DF2_D422N-YTHmut.bed

value: 4hr, 37C, 50ng RNA, 250ng APOBEC1-YTHmut


title: invitro_DART-seq-APOBEC1-YTHmut Replicate 2


title: mIMCD-3 WT cells, treatment 48 h dark, experiment number e19103

value: WT

value: 48 h dark


title: mIMCD-3 WT cells, treatment 48 h dark + Forskolin 10 µM during last hour, experiment number e1994


title: invitro_DART-seq-APOBEC1-YTHmut Replicate 1


title: mIMCD-3 Cilia-bPAC cells, treatment 48 h dark, experiment number e1994


title: mRNA-seq PFC Naïve Rep2

description: mRNA transcripts from PFC Naïve Rep2