title: PBMC_K4me123_AnB_0.25X_(220826_DJ_Hs_PBMC_K4me123_DJnMM_0.25X_220527)

description: sciCUT&Tag for H3K4me123 run on a mixture of PBMCs from healthy donor A and donor B dispensed on the ICELL8 at a concentration of 6 nuclei per nanowell


title: PBMC_K4me123_AnB_0.5X_(220826_DJ_Hs_PBMC_K4me123_DJnMM_0.5X_220527)

status: Public on Jul 13 2023

type: SRA

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: sciCUT&Tag for H3K4me123 run on a mixture of PBMCs from healthy donor A and donor B and dispensed on the ICELL8 at a concentration of 12 nuclei per nanowell

library_source: genomic

data_processing:
Genome_build: hg38
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg38 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the D. melanogaster alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg38 track which is the fraction of counts at each base pair scaled by the size of the hg38 reference sequence (3210038034) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)

molecule: genomic DNA

organism: Homo sapiens

source_name: sciCUT&Tag

tag: scicut&tag antibody

value: A mixture of H3K4me1 Invitrogen cat# 710795, H3K4me2 Millipore cat# 07-030, H3K4me3 Active Motif cat# 39159

tag: human sample


title: SPT16_AID_V5_Clone1_IAA_ATAC_washout_Rep1

city: Pittsburgh

first: David

middle: Charles

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Reads were trimmed to 25 bp and barcode adapter sequences removed using trim_galore
Reads mapped to mm10 genome using bowtie2, allowing for 1 mismatch
Duplicates were removed using Picard
Reads were filtered for quality using SAMtools (MAPQ ≥ 10) and size-selected into nucleosome-free (1-100 bp) size class
Reads were processed in deepTools by using the bamCoverage command to generate bigwig files detailing coverage genome-wide in 1 bp bins with RPGC normalization, using an effectiveGenomeSize of 2308125349
Assembly: mm10
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: cell line

growth_protocol: Murine embryonic stem cells were grown under feeder-free conditions in DMEM, supplemented with 10% Fetal Bovine Serum, 2 mM-Glutamine, 1X non-essential amino acids, 0.129mM 2-mercaptoethanol, 1000U/mL Leukemia Inhibitory Factor (LIF), 3 µM CHIR99021 GSK inhibitor (p212121), and 1 µM PD0325091 MEK inhibitor (p212121). Cells were passaged every 48 hours using trypsin (Gibco) and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened by PCR to confirm no mycoplasma presence.

extract_protocol:
Medium was aspirated and cells were washed with DPBS. DPBS was aspirated and cells were trypsinized. Cells were pelleted, washed with DPBS, and resuspended in hypotonic buffer. Nuclei were pelleted and lysed cell debris (supernatant) removed. Nuclei were flash-frozen until time of use. Nuclei were transposed for 30 minutes at 37C with 100 rpm shaking and Tn5 transposome (Diagenode). Libraries were amplified for 10 cycles of high-fidelity PCR
Transposed for 30 minutes at 37C with 100 rpm shaking and Tn5 transposome (Diagenode). Libraries were amplified for 10 cycles of high-fidelity PCR

treatment_protocol: After 48 hours of undisturbed growth on 10 cm plates, medium was aspirated and cells were washed with DPBS. DPBS was aspirated and fresh medium was added containing 500 nM 3-Indoleacetic acid (3-IAA) or an equivalent volume of 100% ethanol. Plates were then left at 37 degrees Celsius with 5% CO2 for 12 hours, then incubated in fresh medium without treatment for 24 hours before extraction.

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: murine embryonic stem cells

tag: treatment

value: IAA

value: Cells were left undisturbed on 10 cm plates for 48 hours prior to treatment. Cells were treated with 0.1% ethanol mixed into medium for the indicated time (hours). Cells were incubated at 37 degrees Celsius with 5% CO2 for the duration of treatment.


title: PBMC_K4me123_AnB_0.125X_(220826_DJ_Hs_PBMC_K4me123_DJnMM_0.125X_220527)

description: sciCUT&Tag for H3K4me123 run on a mixture of PBMCs from healthy donor A and donor B and dispensed on the ICELL8 at a concentration of 3 nuclei per nanowell


title: N10N11 P3KO-MII-5

city: Shanghai

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

description:
P3KO-MII-5
oocyte_processed_file.xlsx

library_source: transcriptomic

data_processing:
The preprocessing steps of RNA-seq are as follows: The raw paired-end fastq reads were removed adapter and quality-filtered by TrimGalore-0.5.0 with the parameters --paired --quality 20 --phred33 --stringency 1 --length 35. The remaining reads were mapped to the genome or identified TE by STAR v2.9, respectively. Uniquely mapped reads and multiple mapped reads with fewer than 10,000 genome copies were used for downstream analysis. The specific alignment parameters are as follows: --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --twopassMode Basic --outSAMprimaryFlag AllBestScore. Calculate the reads count of known genes or TEs by featureCounts v1.6.4 with the parameters -p -B -C -M -Q 20, The expression of known genes or TEs was normalized to the ERCC or mapped reads. Genes or TEs with normalized count>2 in 40% or more of samples were used for differential analysis. Differentially expressed genes or TEs were identified by applying combined thresholds on the basis of fold change (>4 or <0.25) and permutation test (Padj <= 0.01).
Assembly: hamster: BCM_Maur_2.0, mouse: mm10
Supplementary files format and content: testis_processed_file.xlsx and oocyte_processed_file.xlsx:tab-delimited text files include normalized values by ERCC and gene length for each Sample;
Supplementary files format and content: spermatogenesis_processed_file.xlsx:tab-delimited text files include normalized values by total reads and gene length for each Sample

molecule: total RNA

organism: Mesocricetus auratus

source_name: oocyte

extract_protocol:
Samples were incubated at 72°C for 3 min to release and unfold the small RNAs or RNA.
small RNA libraries construction: Briefly, Samples were incubated at 72°C for 3 min to release and unfold the small RNAs. After 3’ adapter ligation, 5U of lambda exonuclease and 25U of 5’ deadenylases, which performed better than the combination of RecJf and 5’ deadenylases, were used to remove the excess 3’ adaptor. Then, a 5’ adapter was ligated and small RNAs were reverse transcribed. Pre-amplification was performed and then 1 μl of amplified product was used as a template for final amplification. The amplified libraries were separated on a 6% polyacrylamide gel and 130-160 bp DNA fragments were sliced to recover the library of small RNAs.  mRNA library construction:In brief, Samples were incubated at 72°C for 3 min to release the RNAs. For every single oocyte or embryo, 0.125 μL 1/100,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, Cat# 4456740) was used. Following reverse transcription and PCR pre-amplification, cDNA libraries were purified by Agencourt Ampure XP beads (0.8:1 ratio) (Beckman Coulter, Cat#A63881) and 2 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase. Amplified libraries were purified by Agencourt Ampure XP beads (1:1 ratio).

value: oocyte

tag: Sex

value: female

tag: Stage

value: MII

tag: genotype

value: piwil3 -/-


title: 7E_M_494

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: PBMC_K4me123_A_1X_(220826_DJ_Hs_PBMC_K4me123_DJ_1X_220527)

description: sciCUT&Tag for H3K4me123 run on PBMCs from healthy donor A and dispensed on the ICELL8 at a concentration of 24 nuclei per nanowell

tag: scicut&tag antibodies

value: PBMCs from healthy donor A


title: PBMC_K4me123_A_PE79_(220901_DJ_Hs_PBMC_K4me123_DJ_PE79_220523)

description: sciCUT&Tag for H3K4me123 run on PBMCs from healthy donor A


title: 7E_M_493


title: PBMC_K4me123_A_0.5X_(220826_DJ_Hs_PBMC_K4me123_DJ_0.5X_220527)

description: sciCUT&Tag for H3K4me123 run on PBMCs from healthy donor A and dispensed on the ICELL8 at a concentration of 12 nuclei per nanowell


title: 7E_M_492


title: N10N44 P3KO-MII-3

description:
P3KO-MII-3
oocyte_processed_file.xlsx


title: PBMC_K4me123_A_0.25X_(220826_DJ_Hs_PBMC_K4me123_DJ_0.25X_220527)

description: sciCUT&Tag for H3K4me123 run on PBMCs from healthy donor A and dispensed on the ICELL8 at a concentration of 6 nuclei per nanowell


title: N10N43 P3KO-MII-2

description:
P3KO-MII-2
oocyte_processed_file.xlsx


title: PBMC_K4me123_A_0.125X_(220826_DJ_Hs_PBMC_K4me123_DJ_0.125X_220527)

description: sciCUT&Tag for H3K4me123 run on PBMCs from healthy donor A and dispensed on the ICELL8 at a concentration of 3 nuclei per nanowell


title: PBMC_K27me3_B_PE79_(220901_DJ_Hs_PBMC_K27me3_MM_PE79_220523)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor B

value: H3K27me3 Cell Signaling Technologies cat# C36B11

value: PBMCs from healthy donor B


title: N10N42 P3KO-MII-1

description:
P3KO-MII-1
oocyte_processed_file.xlsx


title: 7E_M_491


title: PBMC_K27me3_B_0.5X_(220826_DJ_Hs_PBMC_K27me3_MM_0.5X_220527)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor B and dispensed on the ICELL8 at a concentration of 12 nuclei per nanowell


title: 7E_M_490


title: PBMC_K27me3_B_1X_(220826_DJ_Hs_PBMC_K27me3_MM_1X_220527)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor B and dispensed on the ICELL8 at a concentration of 24 nuclei per nanowell


title: PBMC_K27me3_B_0.25X_(220826_DJ_Hs_PBMC_K27me3_MM_0.25X_220527)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor B and dispensed on the ICELL8 at a concentration of 6 nuclei per nanowell


title: PBMC_K27me3_B_0.125X_(220826_DJ_Hs_PBMC_K27me3_MM_0.125X_220527)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor B and dispensed on the ICELL8 at a concentration of 3 nuclei per nanowell


title: 7E_M_489


title: N10N40 P3KO-GV-4

description:
P3KO-GV-4
oocyte_processed_file.xlsx

value: GV


title: PBMC_K27me3_AnB_1X_(220826_DJ_Hs_PBMC_K27me3_DJnMM_1X_220527)

description: sciCUT&Tag for H3K27me3 run on a mixture of PBMCs from healthy donor A and donor B and dispensed on the ICELL8 at a concentration of 24 nuclei per nanowell


title: N10N41 P3KO-GV-5

description:
P3KO-GV-5
oocyte_processed_file.xlsx


title: PBMC_K27me3_AnB_0.5X_(220826_DJ_Hs_PBMC_K27me3_DJnMM_0.5X_220527)

description: sciCUT&Tag for H3K27me3 run on a mixture of PBMCs from healthy donor A and donor B and dispensed on the ICELL8 at a concentration of 12 nuclei per nanowell


title: PBMC_K27me3_AnB_PE79_(220901_DJ_Hs_PBMC_K27me3_DJnMM_PE79_220523)

description: sciCUT&Tag for H3K27me3 run on a mixture of PBMCs from healthy donor A and donor B


title: N10N38 P3KO-GV-2

description:
P3KO-GV-2
oocyte_processed_file.xlsx


title: 7E_M_487


title: PBMC_K27me3_AnB_0.25X_(220826_DJ_Hs_PBMC_K27me3_DJnMM_0.25X_220527)

description: sciCUT&Tag for H3K27me3 run on a mixture of PBMCs from healthy donor A and donor B dispensed on the ICELL8 at a concentration of 6 nuclei per nanowell


title: 7E_M_486


title: N10N33 WT-54PEA-5

description:
WT-54PEA-5
oocyte_processed_file.xlsx

source_name: embryo

value: embryo

value: wild type


title: 7E_M_488


title: PBMC_K27me3_A_PE79_(220901_DJ_Hs_PBMC_K27me3_DJ_PE79_220523)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor A


title: 7E_M_485


title: PBMC_K27me3_A_1X_(220826_DJ_Hs_PBMC_K27me3_DJ_1X_220527)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor A and dispensed on the ICELL8 at a concentration of 24 nuclei per nanowell


title: PBMC_K27me3_A_0.5X_(220826_DJ_Hs_PBMC_K27me3_DJ_0.5X_220527)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor A and dispensed on the ICELL8 at a concentration of 12 nuclei per nanowell


title: PBMC_K27me3_AnB_0.125X_(220826_DJ_Hs_PBMC_K27me3_DJnMM_0.125X_220527)

description: sciCUT&Tag for H3K27me3 run on a mixture of PBMCs from healthy donor A and donor B and dispensed on the ICELL8 at a concentration of 3 nuclei per nanowell


title: 7E_M_484


title: 7E_M_483


title: N10N28 WT-34PEA-5

description:
WT-34PEA-5
oocyte_processed_file.xlsx


title: N10N27 WT-34PEA-4

description:
WT-34PEA-4
oocyte_processed_file.xlsx


title: PBMC_K27me3_A_0.25X_(220826_DJ_Hs_PBMC_K27me3_DJ_0.25X_220527)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor A and dispensed on the ICELL8 at a concentration of 6 nuclei per nanowell


title: N10N26 WT-34PEA-3

description:
WT-34PEA-3
oocyte_processed_file.xlsx


title: 7E_M_482


title: 7E_M_481


title: A.024

type: RNA

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Samples were hybridized for 16 hours at 65C

scan_protocol: Detection and scanning were performed by the nCounter SPRINT Profiler analysis system.

label: fluorescence microscope

source_name: FFPE

label_protocol: Sample RNA is hybridized with target-specific capture and reporter probes. This creates a library of unique target-probe complexes. Each target is labelled with a specific barcode, which can be detected and counted using an automated fluorescence microscope.

extract_protocol: AllPREP FFPE DNA/RNA kit (Qiagen) according to manufacturer's protocol

value: adenoma


title: T.024

data_processing: Detection and scanning were performed by the nCounter SPRINT Profiler analysis system.

value: tumor


title: N10N21 WT-34PEA-1

description:
WT-34PEA-1
oocyte_processed_file.xlsx


title: A.021


title: T.021


title: 7E_M_480


title: N10N19 WT-11PEA-3

description:
WT-11PEA-3
oocyte_processed_file.xlsx


title: N10N29 WT-54PEA-1

description:
WT-54PEA-1
oocyte_processed_file.xlsx


title: A.017


title: N10N18 WT-11PEA-2

description:
WT-11PEA-2
oocyte_processed_file.xlsx


title: 7E_M_479


title: 7E_M_478


title: N10N17 WT-11PEA-1

description:
WT-11PEA-1
oocyte_processed_file.xlsx


title: PBMC_K27me3_A_0.125X_(220826_DJ_Hs_PBMC_K27me3_DJ_0.125X_220527)

description: sciCUT&Tag for H3K27me3 run on PBMCs from healthy donor A and dispensed on the ICELL8 at a concentration of 3 nuclei per nanowell


title: A.016


title: T.016


title: 7E_M_477


title: A.013


title: N10N16 WT-11PEA-3-8PEA

description:
WT-11PEA-3-8PEA
oocyte_processed_file.xlsx


title: T.013


title: A.012


title: A.014


title: 7E_M_476


title: T.012


title: T.014


title: A.010


title: 7E_M_475


title: T.017


title: 7E_M_474


title: A.009


title: N10N09 WT-MII-4

description:
WT-MII-4
oocyte_processed_file.xlsx


title: N10N07 WT-MII-2

description:
WT-MII-2
oocyte_processed_file.xlsx


title: 7E_M_473


title: 7E_M_472


title: N10N06 WT-MII-1

description:
WT-MII-1
oocyte_processed_file.xlsx


title: A.004


title: T.004


title: T.003


title: N10N14 WT-11PEA-1-8PEA

description:
WT-11PEA-1-8PEA
oocyte_processed_file.xlsx


title: A.001


title: 7E_M_470


title: T.001


title: 7E_M_471


title: N10N13 WT-MII-5

description:
WT-MII-5
oocyte_processed_file.xlsx


title: T.010


title: N10N01 WT-GV-1

description:
WT-GV-1
oocyte_processed_file.xlsx


title: T.024


title: A.023


title: 7E_M_469


title: N10N03 WT-GV-3

description:
WT-GV-3
oocyte_processed_file.xlsx


title: A.022


title: 7E_M_468


title: T.023


title: T.009


title: T.022


title: A.003


title: F1R52 P3KO-54PEA-4

description:
P3KO-54PEA-4
smRNA_piRNA_file.zip

data_processing:
The preprocessing steps of smRNA-seq are as follows: intercept the first 50bp of reads and filter out low-quality sequences (-q 20, -p 90); After quality-filtering, sequencing reads were clipped from the 3′ adapter allowing for a minimum match of 10 nt from the 5′ end. Reads unable to match the adapter sequence or with lengths shorter than 17 bp were discarded, and the remaining reads were mapped to genome by bowtie (hamster: BCM_Maur_2.0, mouse: mm10), bowtie version 1.2.1.1, parameters -k=100 -v=0). If the reads mapped more than 100 loci to the genome, 100 of all mapped loci are randomly output. The reads were aligned sequentially to known miRNA, tRNA, rRNA, snoRNA, and snRNA sequences by Bowtie without any mismatch allowed (bowtie parameter is -k=100 -v=0 -norc), and reads that aligned to pre-miRNA were identified as miRNAs. The remaining reads of the specified length were extracted and used to identify piRNAs according to the previously described method (Jung et al. 2014) with slight modifications. The length of candidate piRNAs in male samples is 25~32nt, and the length of candidate piRNAs in female samples is 17~32nt. The clustering parameters were determined as MinReads = 5 and Eps = 2500 bp by running a series of k-dist analyses of our data with different Eps and MinReads. All of the candidate clusters that satisfied these parameters were considered piRNA clusters, and the remaining sequences located in these clusters were defined as piRNAs without any further filtering. Reads in each library were normalized by sequencing depth or reads count of miRNA or reads count of exogenous spike-in.
The preprocessing steps of RNA-seq are as follows: The raw paired-end fastq reads were removed adapter and quality-filtered by TrimGalore-0.5.0 with the parameters --paired --quality 20 --phred33 --stringency 1 --length 35. The remaining reads were mapped to the genome or identified TE by STAR v2.9, respectively. Uniquely mapped reads and multiple mapped reads with fewer than 10,000 genome copies were used for downstream analysis. The specific alignment parameters are as follows: --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --twopassMode Basic --outSAMprimaryFlag AllBestScore. Calculate the reads count of known genes or TEs by featureCounts v1.6.4 with the parameters -p -B -C -M -Q 20, The expression of known genes or TEs was normalized to the ERCC or mapped reads. Genes or TEs with normalized count>2 in 40% or more of samples were used for differential analysis. Differentially expressed genes or TEs were identified by applying combined thresholds on the basis of fold change (≥2 or ≤0.5) and Welch two-sample t-test (P ≤ 0.05).
Assembly: hamster: BCM_Maur_2.0, mouse: mm10
Supplementary files format and content: testis_processed_file.xlsx and oocyte_processed_file.xlsx:tab-delimited text files include normalized values by ERCC and gene length for each Sample;
Supplementary files format and content: spermatogenesis_processed_file.xlsx:tab-delimited text files include normalized values by total reads and gene length for each Sample


title: A.021


title: T.021


title: N10N04 WT-GV-4

description:
WT-GV-4
oocyte_processed_file.xlsx


title: A.024


title: F1R47 P3KO-34PEA-5

description:
P3KO-34PEA-5
smRNA_piRNA_file.zip


title: 7E_M_466


title: A.019


title: A.020


title: T.020


title: 7E_M_465


title: T.019


title: F1R45 P3KO-34PEA-3

description:
P3KO-34PEA-3
smRNA_piRNA_file.zip


title: 7E_M_464


title: F1R43 P3KO-34PEA-1

description:
P3KO-34PEA-1
smRNA_piRNA_file.zip


title: F1R42 P3KO-11PEA-5

description:
P3KO-11PEA-5
smRNA_piRNA_file.zip


title: A.007


title: T.018


title: A.018


title: 7E_M_467


title: A.017


title: T.017


title: 7E_M_462


title: F1R41 P3KO-11PEA-4

description:
P3KO-11PEA-4
smRNA_piRNA_file.zip


title: F1R40 P3KO-11PEA-3

description:
P3KO-11PEA-3
smRNA_piRNA_file.zip


title: 7E_M_461


title: T.016


title: A.016


title: 7E_M_460


title: A.015


title: T.015


title: F1R39 P3KO-11PEA-2

description:
P3KO-11PEA-2
smRNA_piRNA_file.zip


title: F1R38 P3KO-11PEA-1

description:
P3KO-11PEA-1
smRNA_piRNA_file.zip


title: F1R50 P3KO-54PEA-2

description:
P3KO-54PEA-2
smRNA_piRNA_file.zip


title: 7E_M_463


title: 7E_M_459


title: A.003


title: T.014


title: 7E_M_457


title: 7E_M_458


title: F1R37 P3KO-MII-5

description:
P3KO-MII-5
smRNA_piRNA_file.zip


title: A.013


title: A.014


title: F1R35 P3KO-MII-3

description:
P3KO-MII-3
smRNA_piRNA_file.zip


title: A.012


title: T.012


title: 7E_M_456


title: F1R34 P3KO-MII-2

description:
P3KO-MII-2
smRNA_piRNA_file.zip


title: 7E_M_454


title: F1R33 P3KO-MII-1

description:
P3KO-MII-1
smRNA_piRNA_file.zip


title: A.009


title: T.010


title: A.010


title: 7E_M_452


title: T.011


title: A.008


title: F1R31 P3KO-GV-4

description:
P3KO-GV-4
smRNA_piRNA_file.zip


title: T.008


title: T.013


title: T.009


title: F1R29 P3KO-GV-2

description:
P3KO-GV-2
smRNA_piRNA_file.zip


title: F1R27 WT-54PEA-5

description:
WT-54PEA-5
smRNA_piRNA_file.zip


title: A.005


title: F1R23 WT-54PEA-1

description:
WT-54PEA-1
smRNA_piRNA_file.zip


title: T.006


title: T.007


title: 7E_M_449


title: A.006


title: F1R32 P3KO-GV-5

description:
P3KO-GV-5
smRNA_piRNA_file.zip


title: 7E_M_453


title: A.004


title: 7E_M_448


title: 7E_M_450


title: T.004


title: A.011


title: F1R22 WT-34PEA-5

description:
WT-34PEA-5
smRNA_piRNA_file.zip


title: 7E_M_447


title: T.005


title: T.003


title: 7E_M_451


title: A.002


title: F1R21 WT-34PEA-4

description:
WT-34PEA-4
smRNA_piRNA_file.zip


title: A.001


title: 7E_M_446


title: T.001


title: Mouse rescue colonic mucosa: injected with miR-10b-5p mimic in global mir-10b-/-

city: Reno

first: Seungil

last: Ro

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada Reno

description:
Colon_mucosa_mimic
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing 50bp on an Illumina Hiseq 2500 at the LC Sciences (Hangzhou, China) following the vendor's recommended protocol.

data_processing:
Raw data were filtered using a filter module in a in-house program ACGT101-miR to delete low-quality reads, 3' adapter sequences, and contaminations. The sequences ≥18 nt of clean data were annotated in the Rfam database to remove non-coding RNA (rRNA, tRNA, snRNA, snoRNA) and degradation fragments of mRNA. The remaining sequences were aligned against miRNA database, miRbase and perfectly matched sequences were considered conserved Mus musculus miRNAs.
Assembly: mm10
Supplementary files format and content: Excel

source_name: Colon Mucosa

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing 50bp on an Illumina Hiseq 2500 at the LC Sciences (Hangzhou, China) following the vendor's recommended protocol.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon Mucosa

value: global mir-10b-/-

value: miR-10b-5p mimic


title: Mouse diabetic colonic mucosa: global mir-10b-/-

description:
Colon_mucosa_KO
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing 50bp on an Illumina Hiseq 2500 at the LC Sciences (Hangzhou, China) following the vendor's recommended protocol.


title: 7E_M_445


title: F1R18 WT-34PEA-1

description:
WT-34PEA-1
smRNA_piRNA_file.zip


title: Mouse healthy colonic mucosa: global mir-10b+/+

description:
Colon_mucosa_WT
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing 50bp on an Illumina Hiseq 2500 at the LC Sciences (Hangzhou, China) following the vendor's recommended protocol.

value: global mir-10b+/+


title: untreated HUVEC replicate 4

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides.
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a
Aligned reads were filtered to remove: duplicates with Picard 2.25.5, multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes. The raw count matrix was normalized with DESeq2 version 1.30.1
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: hg38
Supplementary files format and content: library size normalized count matrix

source_name: human umbilical vein endothelial cells

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).

treatment_protocol: no treatment or stimulation after antibiotic selection

value: HUVEC


title: 7E_M_444


title: F1R16 WT-11PEA-3

description:
WT-11PEA-3
smRNA_piRNA_file.zip


title: Human_MR+AF_5

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

description:
FACS-purified left atrial non-cardiomyocytes
mRNA

data_processing:
Illumina proprietary software used for basecalling.
10X Genomics Cell Ranger (version 6.0.2 for human samples, version 3.0.2 for mouse samples) was used to demultiplex raw base call files from the Illumina sequencer to produce fastq files.
Cell Ranger was used to align the reads, filter out background-associated-barcodes, count barcodes and UMIs, and generate gene-barcode matrices.
Genome_build: GRCh38 for human samples, GRCm38 (mm10) for mouse samples.
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.tar.gz: tar archives include matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz files; Count matrices in Market Exchange Format for sparse matrices and gzipped tsv files for genes and barcodes corresponding to row and column indices of the count matrices.

source_name: Heart

extract_protocol:
Viable (DAPI-), metabolically active (Calcein+), nucleated (VDR+), single cells were FACS-purified from digested left atrial tissues, and subsequently loaded on a 10X Genomics Chromium Single Cell B chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics). Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR, and subsequently sequenced on an Illumina NextSeq 500 in high-output mode.

tag: disease status

value: moderate to severe mitral valve regurgitation + persistent atrial fibrillation

value: male

value: left atrial appendage

value: non-cardiomyocytes


title: 7E_M_442


title: 7E_M_441


title: Human_MR+AF_6


title: untreated HUVEC replicate 1


title: F1R14 WT-11PEA-1

description:
WT-11PEA-1
smRNA_piRNA_file.zip

value: female


title: 7E_M_443


title: Human_MR+AF_7


title: F1R13 WT-11PEA-3-8PEA

description:
WT-11PEA-3-8PEA
smRNA_piRNA_file.zip


title: T.002


title: Intratumoral cDC

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

description:
Conventional dendritic cells sorted from murine tumors
Targeted scRNA-Seq (BD Rhapsody)

library_source: transcriptomic single cell

data_processing:
The raw sequencing reads were processed on the Seven Bridges platform with the BD Rhapsody Targeted Analysis pipeline v1.8 using the default parameters.
Filtering: Cells with less than 5 genes detected were removed from the analysis, as well as cells with more than 500 molecule counts.
Normalization: The output filtered molecule counts after adjustment with distribution-based error correction (DBEC) were log-normalized and regressed on the number of molecules detected per cell using Seurat v3.1.1.
Dimensional reduction: All detected features were used for linear dimensional reduction by PCA. Thirty nearest neighbors were computed for each cell using the first 7 principal components (or 6 for filtered data set), which were also used for non-linear dimensionality reduction by tSNE (perplexity 60).
Clustering: Clusters were identified with the Louvain algorithm (resolution 0.6).
Assembly: Reads were aligned to a custom reference (see supplementary file "amplicons.fasta").
Supplementary files format and content: The comma delimited file (.csv) contains the output from the BD Rhapsody Targeted Analysis pipeline after filtering and adjustment with distribution-based error correction (DBEC). Rows correspond to cell indices and columns correspond to genes.
Supplementary files format and content: The Excel files (.xlsx) contain metadata for each cell and normalized or scaled gene expression for cells before or after filtering out contaminating cells.

source_name: tumor

extract_protocol:
On day 6 of tumor growth, tumors were extracted and a single-cell suspension was prepared according to standard protocols. Cells were stained with fluorescently-labelled antibodies and conventional dendritic cells were sorted using a FACSAria Sorter (BD). Single-cell RNA was then extracted using the BD Rhapsody Single-Cell Analysis System.
RNA libraries were prepared using the BD Rhapsody Single-Cell Analysis System, following manufactrurer's instructions, and standard Illumina protocols adding 15% PhiX for sequencing. The BD Mouse Inflammatory response panel was supplemented with a custom set of primers to include additional genes in the analysis (see  supplementary file "supplementary_panel.xlsx").

treatment_protocol: 2x10^6 BRAFV600E Ptgs1/Ptgs2-/- tumor cells were injected subcutaneously into the flanks of C57BL/6 mice.

value: BRAFV600E Ptgs1/Ptgs2 -/-


title: F1R20 WT-34PEA-3

description:
WT-34PEA-3
smRNA_piRNA_file.zip


title: Human_MR+AF_4


title: untreated HUVEC replicate 2


title: F1R11 WT-11PEA-1-8PEA

description:
WT-11PEA-1-8PEA
smRNA_piRNA_file.zip


title: Human_MR+AF_3


title: 7E_M_439


title: 7E_M_440


title: untreated HUVEC replicate 3


title: Human_MR+AF_1


title: F1R10 WT-MII-5

description:
WT-MII-5
smRNA_piRNA_file.zip

value: oocyte

value: MII


title: 7E_M_438


title: F1R15 WT-11PEA-2

description:
WT-11PEA-2
smRNA_piRNA_file.zip

value: embryo


title: Human_control_4

value: control


title: Human_control_5


title: Human_control_3


title: F1R7 WT-MII-2

description:
WT-MII-2
smRNA_piRNA_file.zip

value: wild type


title: Human_control_2


title: Human_control_1


title: 7E_M_437


title: Human_MR+AF_2


title: 7E_M_434


title: 7E_M_436


title: F1R3 WT-GV-3

description:
WT-GV-3
smRNA_piRNA_file.zip

value: GV


title: 7E_M_432


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S9_CGATGT

city: Philadelphia

first: Hao

last: Wu

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

data_processing:
The pre-processing (read alignment, quality filtering and read deduplication) was performed for snhmC/Joint-snhmC-seq datasets of individual single cells as previously described with minor modifications6. Briefly, demultiplexing of inline barcodes was first performed allowing up to 1-nt mismatch. The data quality was examined with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw sequencing reads were trimmed for adaptor sequences and inline barcodes using Cutadapt with the following parameters in paired-end mode: -f fastq -q 20 -u 16 -U 16 -m 30 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. The trimmed R1 and R2 reads were mapped independently against the reference genome (mm10) using Bismark (v0.18.2) with following parameters: --bowtie2 -D 15 -R 2 -L 20 -N 0 –score_min L,0,-0.2 (--pbat option was turned on for mapping R1 reads). Uniquely mapped reads were filtered for minimal mapping quality (MAPQ>=10) using samtools9. PCR duplicates were removed using the Picard MarkDuplicates (http://broadinstitute.github.io/picard/). To eliminate reads from strands not deaminated by A3A, reads with three or more consecutive non-converted cytosines in the CH context were removed using filter_non_conversion in Bismark. Low quality snhmC/Joint-snhmC-seq datasets were removed using the following set of criteria. First, Mapping rate of raw sequencing reads is set to be at least 20%; Second, we set a minimum on the number of pass filter reads (uniquely mapped, deduplicated, MAPQ>=10, <=3 consecutive 5mCH sites) to be 100,000 per cell; Third, the 5mCG deamination rate in spike-in lambda phage control is higher than 90%. Base calling of unmethylated and methylated cytosines was performed by bismark_methylation_extractor in Bismark in each individual nucleus. 5hmC signals were calculated as % of C/(C+T) at each cytosine base.
Assembly: mm10
Supplementary files format and content: Tab-delimited bismark methylation calling files include genomic coordinates (columan 1-3: chromosome, start, and end), 5hmC signal (column 4: % of 5hmC levels normalized to total reads), 5hmC read (column 5), and unmodified read (column 6) for all detected CpG (._CpG.mm10.bismark.cov)  or CpH (._CpH.mm10.bismark.cov) sites across the mouse genome in individually sequenced cell.
Library strategy: bisulfite-assisted ACE-seq

source_name: Cortex

growth_protocol: All experiments were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) at the University of Pennsylvania. Mice were group-housed in cages of three to five in a 12-hr light/dark cycle with food and water provided ad libitum. All mice used for experiments were naïve to behavioral assays and other procedures. For all bulk-nucleus and single-nucleus experiments, 6-10 weeks old, wild-type, male mice in a pure C57BL/6J background were used. For prospectively isolating inhibitory (Inh) and excitatory (Ex) neuronal subtypes to benchmark snhmC-seq and joint-snhmC-seq, 9-week-old transgenic mice (Mecp2Tavi/y, NexCre/+, Rosa26BirA/BirA) from a C57BL/6J background were used as previously described (Johnson et al. 2017; PMID: 28920956).

extract_protocol:
Nuclei isolation from mouse cortical tissues was performed as described with minor modifications (Hu* & Fabyanic* et al., 2017; PMID: 29220646). Briefly, mouse brains were rapidly resected on ice. Cortices were flash-frozen in liquid nitrogen and stored at -80°C before nuclear isolation. Nuclei were isolated and purified as previously described with some modifications3. Briefly, 14mL sucrose cushion (1.8M sucrose (Sigma-Aldrich, RNase and DNase free, ultra-pure grade), 10mM Tris-HCl pH 8.0, 3mM MgAc2 (Sigma-Aldrich), and protease inhibitor cocktail (Roche)) was added to the bottom of centrifuge tubes (Beckman Coulter). Using a glass homogenizer (Wheaton), a frozen mouse cortical sample was dounce homogenized (19 times with loose pestle followed by 4 times with tight pestle) in 12mL homogenization buffer (0.32M sucrose, 5mM CaCl2 (Sigma-Aldrich), 3mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton X-100 (Sigma-Aldrich), 0.1mM EDTA (Invitrogen), protease inhibitor cocktail (Roche)). Homogenates (~12ml) were carefully layered onto the sucrose cushion in the centrifuge tubes, and 10mL homogenization buffer was added atop of the homogenates. The tubes were then balanced and centrifuged in a Beckman Coulter L7-65 Ultracentrifuge at 82,705 g at 4°C for 2hr using a Beckman Coulter SW28 swing bucket rotor (Beckman Coulter). The supernatant was carefully removed via aspiration. 1ml chilled DPBS was added to resuspend the nuclear pellet, and nuclei were subsequently transferred to a 1.5-mL tube. Nuclei were pelleted at 500 g for 10 min at 4C, and then resuspended in 0.01% BSA (Sigma-Aldrich) in DPBS. After resuspension, nuclei were filtered through a 40-μm cell strainer (Fisher Scientific), visually inspected for morphology and quality assurance, and counted using a Fuchs-Rosenthal counting chamber before FANS.
All steps of library preparation were performed in a horizontal laminar flow hood (AirCleanⓇ600 PCR Workstation) to minimize environmental DNA contamination. Bisulfite conversion of bulk nuclei was carried out using the EZ DNA Methylation-Direct™ Kit (Zymo, D5020). Bisulfite conversion of single nucleus was carried out using the EZ-96 DNA Methylation-Direct™ Kit (Zymo, Deep Well Format, D5023). PCR tubes containing FANS-isolated nuclei (100-10,000 nuclei), or 96-well plates containing FANS-isolated single nuclei, were heated at 50°C for 20min. 130μL (for bulk) or 32.5μL (for single nuclei) CT Conversion Reagent was added to each well, followed by pipetting up and down to mix. Plates were treated with the following program using a thermocycler: 98°C for 8min, 64°C for 3.5h, and 4°C forever. Zymo-Spin™ columns or Zymo-Spin™ I-96 Binding Plates were preloaded with either 600μl (bulk) or 250μl (single nuclei) M-binding buffer, respectively. Both bulk and single-cell samples were further purified according to their respective kit instructions, except Low EDTA TE Buffer (IDT) was used as the elution buffer. To perform A3A deamination, 3 µl of denaturing buffer (1.5µl 200mM MES buffer (pH 6.0) with 0.1% Tween-20 and 1.5µl DMSO) was first added to the 9μl eluent retained or each sample. The samples were denatured at 95°C for 1min and snap cooled by transfer to a PCR tube rack pre-incubated at −80°C (for bulk samples) or transfer to an isopropanol dry ice bath and then to the −80°C pre-incubated PCR tube rack (for 96-well plates containing single nuclei). Before thawing, 3 µl of enzymatic reaction mix (1.5µl 200 mM buffer (pH 6.0) with 0.1% Tween-20 and 1.5µl 5μM in-house A3A) was added to each reaction (for a final concentration of 500nM/µl A3A in 15 µl). The deamination reactions were incubated at 37°C for 2h, purified with 1.6x homebrew SPRI beads, eluted in 9µL Low EDTA TE buffer (IDT). To perform random priming and add inline barcodes, 1µL of individual 250µM random primer (with 8-plex inline barcodes: P5L_AD002_H, P5L_AD006_H, P5L_AD008_H, P5L_AD010_H, P5L_AD001_H, P5L_AD004_H, P5L_AD007_H, or P5L_AD012_H) was added to each reaction to allow for subsequent multiplexing reactions during downstream library preparation. Reactions or plates were heated at 95°C using a thermocycler for 3 min to denature and were immediately chilled on ice for 2 min. 10µl enzyme mix (2µl Blue Buffer (Enzymatics B0110), 1µl 10mM dNTP (NEB N0447L), 1µl Klenow (3′→ 5′ exo-) (50U/µl, Enzymatics P7010-HC-L), and 6µl water) was added to each well (a 20µl reaction) and reactions were mixed by vortexing. Plates or reactions were treated with the following program using a thermocycler: 4°C for 5min, ramp up to 25°C at 0.1°C/sec, 25°C for 5min, ramp up to 37°C at 0.1°C/sec, 37°C for 60min, 4°C forever. Next, 2μl Exonuclease 1 (20U/μl, Enzymatics X8010L) and 1μl Shrimp Alkaline Phosphatase (rSAP) (1U/μl, NEB M0371L) was added to each reaction followed by vortexing and incubation in a thermocycler at 37°C for 30min followed by 4°C forever. To multiplex subsequent adaptor ligation reactions, 18.4μl (0.8x) homebrew SPRI beads were added to each reaction and 8 sample/bead mixtures were pooled (up to 24 samples if all inline barcodes were used). The sample/bead mixtures were incubated at room temperature for 5min before being placed on a 96-well magnetic separator (DynaMag™-96 Side Magnet, ThermoFisher 12331D). Supernatant was removed from each well, followed by three rounds of washing with 180μl 80% ethanol. Beads were air dried at room temperature and 10μl Low EDTA TE buffer (IDT) was added to each well to fully resuspend the beads. Eluted samples were then transferred to either new PCR strips (for bulk sample) or 96-well plates (for single nuclei). The reactions were denatured in a thermocycler at 95°C for 3min and subsequently chilled on ice for 2min. 10.5μl Adaptase master mix (2μl Buffer G1, 2μl Reagent G2, 1.25μl Reagent G3, 0.5μl Enzyme G4, 0.5μl Enzyme G5, and 4.25μl Low EDTA TE buffer from xGenTM Methyl-Seq Lib Prep kit, IDT, 10009860) was added to each reaction, followed by vortexing. Reactions were incubated in a thermocycler at 37°C for 30min then 4°C forever. Finally, to amplify the pooled library and add dual indexing barcodes, 30μl PCR mix (25μl KAPA HiFi HotStart ReadyMix, Roche/KAPA Biosystems KK2602, 1μl of 30μM P5 indexing primer, and 5μl of 10μM P7 indexing primer; P5 (D501-508) and P7 (D701-712) indexing primers are listed in Supplementary Sequence 3) were added to each well, followed by mixing with vortexing. Reactions were transferred to a thermocycler programmed with the following stages: 95°C for 2min, 98°C for 30sec, 15 cycles of [98°C for 15sec, 64°C for 30sec, 72°C for 2min] (for pooled single nucleus reactions), 72°C for 5min, and 4°C forever. For bulk samples, we perform qPCR and subtract two cycles from the inflection point for each sample to determine optimal cycle number for amplification. PCR products were cleaned with two rounds of 0.8x SPRI beads, concentration was determined via QbitⓇ dsDNA High Sensitivity Assay Kit (Invitrogen Q32851), and library size was determined via Bioanalyzer (Agilent High Sensitivity DNA Kit, 5067-4626). Reactions were sequenced on Illumina NextSeq 500 (300-cycle High Output v2 Kit) or NovaSeq 6000 (300-cycle v1 kit) sequencers.

value: Cortex

tag: developmental stage

value: 6-10 weeks

value: Male

value: wild-type


title: N10N79 P4KO-MII-4

description:
P4KO-MII-4
oocyte_processed_file.xlsx

value: piwil4 -/-


title: F1R4 WT-GV-4

description:
WT-GV-4
smRNA_piRNA_file.zip


title: 7E_M_435


title: F1R6 WT-MII-1

description:
WT-MII-1
smRNA_piRNA_file.zip


title: 7E_M_433


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S9_TAGCTT


title: Fb_647

city: Munich

last: Engelhardt

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

institute: Technical University Munich

description: cell lysate

data_processing:
Single-end run (SE50) run was performed using a HiSeq2500, MiSeq or a NextSeq 500.
Most steps of this pipeline were performed using the Galaxy platform.
MirDeep2 2.0.0. was used for identification and quantification of microRNAs between samples.
Assembly: mm10
Supplementary files format and content: raw microRNA counts in txt.format

source_name: lung

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions or the cell lysate was used.
Libraries were generated using GenXPro TrueQuant SmallRNA Seq Kit for Ultra Low Input or using NEBNext® Small RNA Library Prep Set for Illumina according to manufacturer's instructions.

value: lung

value: Fibroblasts

value: WT

value: no treatment


title: F1R1 WT-GV-1

description:
WT-GV-1
smRNA_piRNA_file.zip

value: female


title: 7E_M_431


title: N10N77 P4KO-MII-2

description:
P4KO-MII-2
oocyte_processed_file.xlsx


title: WT brains (including cortex and corpus callosum) from 3 mice, combined, scRNA-seq

city: Tainan

first: Chih-Yen Wang

last: Wang

address: No.1, University Rd

department: Biotechnology and Bioindustry Sciences

country: Taiwan

institute: National Cheng Kung University

description:
Daam2-WT
10x Genomics

data_processing:
The scRNA-seq data were processed with Cell Ranger Count v6.1.2 followed by R-studio. Cells with more than 7% mitochondrial RNA or less than 1000 total RNA counts were excluded from data.
Assembly: mm10
Supplementary files format and content: Daam2_WT_E.rds: Integrated matrix data (Daam2_WT vs. Daam2_E).

source_name: brain (including cortex and corpus callosum)

extract_protocol:
P21 mouse cortical tissues from WT and the E-mutant containing corpus callosum (3 animals combined per group) were dissociated with papain at 37 degree for 30 min. Cell solution was prepared using debris and dead cell removal kit with MS separation columns.
Single cell gene expression library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics) by Single Cell Genomic Core (SCG) at the Baylor College of Medicine.
Protocol was based on the instruction (single cell 3' V2; 10x Genomics).

value: all cells included


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S9_ACTTGA


title: Daam2-E-mutant brain (including cortex and corpus callosum) from 3 mice, combined, scRNA-seq

description:
Daam2-E
10x Genomics


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S9_ATCACG


title: F1R9 WT-MII-4

description:
WT-MII-4
smRNA_piRNA_file.zip

value: oocyte


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S8_CGATGT


title: N10N75 P2KO-MII-5

description:
P2KO-MII-5
oocyte_processed_file.xlsx

value: MII

value: piwil2 -/-


title: 7E_M_430


title: 7E_M_429


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S8_CAGATC


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S8_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S7_TGACCA


title: 7E_M_428


title: N10N69 P2KO-MII-2

description:
P2KO-MII-2
oocyte_processed_file.xlsx


title: 7E_M_427


title: N10N89 WT-MII2-2

description:
WT-MII2-2
oocyte_processed_file.xlsx


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S6_CGATGT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S7_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S7_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S6_ACTTGA


title: F1R62 P4KO-MII-4

description:
P4KO-MII-4
smRNA_piRNA_file.zip


title: N10N90 WT-MII2-3

description:
WT-MII2-3
oocyte_processed_file.xlsx


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S5_CGATGT


title: 7E_M_425


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S5_TGACCA


title: 7E_M_426


title: 7E_M_424


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S7_CTTGTA


title: 7E_M_423


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S8_CTTGTA


title: F1R60 P4KO-MII-2

description:
P4KO-MII-2
smRNA_piRNA_file.zip


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S5_CAGATC


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S5_ATCACG


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S5_GCCAAT


title: N10N73 P2KO-MII-3

description:
P2KO-MII-3
oocyte_processed_file.xlsx


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S5_ACTTGA


title: 7E_M_422


title: F1R59 P4KO-MII-1

description:
P4KO-MII-1
smRNA_piRNA_file.zip


title: 7E_M_421


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S6_GCCAAT


title: N10N88 WT-MII2-1

description:
WT-MII2-1
oocyte_processed_file.xlsx


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S4_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S4_CGATGT


title: 7E_M_419


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S3_CTTGTA


title: 7E_M_420


title: F1R55 P2KO-MII-2

description:
P2KO-MII-2
smRNA_piRNA_file.zip


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S3_TAGCTT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S3_ATCACG


title: 7E_M_417


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S4_ACTTGA


title: F1R56 P2KO-MII-3

description:
P2KO-MII-3
smRNA_piRNA_file.zip


title: F1R70 WT-MII2-3

description:
WT-MII2-3
smRNA_piRNA_file.zip


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S3_ACTTGA


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S3_GCCAAT


title: F1R69 WT-MII2-2

description:
WT-MII2-2
smRNA_piRNA_file.zip


title: 7E_M_418


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S3_CGATGT


title: F1R68 WT-MII2-1

description:
WT-MII2-1
smRNA_piRNA_file.zip


title: 7E_M_416


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S2_TAGCTT


title: 7E_M_415


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S2_TGACCA


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S2_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S4_CTTGTA


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S2_CGATGT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S2_CTTGTA


title: F1R58 P2KO-MII-5

description:
P2KO-MII-5
smRNA_piRNA_file.zip


title: 7E_M_414


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S2_CAGATC


title: 3_ARC_input

city: New Haven

first: Thomas

middle: David

last: Manes

state: CT

address: 10 Amistad St.

department: Immunobiology

institute: Yale University School of Medicine

data_processing:
The quality of the unaligned reads was assessed to identify any potential issues with the sequence reads.
Trimming of adapter sequences and low-quality bases was performed to obtain clean reads.
The trimmed paired-end reads were aligned to the hg38 reference genome using the STAR aligner tool in Partek Flow.
The quality of the aligned reads was assessed to determine the alignment rate and coverage.
To quantify gene expression levels, aligned reads were processed using Partek Flow's built-in quantification module, which uses the annotation file corresponding to the reference genome to assign reads to known transcripts or genes. Genes with low expression (< 10 counts) were filtered out to reduce noise. Filtered counts were normalized by feature according to Partek Flow’s default settings. The resulting counts were used as input for further expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include filtered counts normalized by feature for each sample

source_name: peripheral blood

extract_protocol:
Rneasy Plus Mini Kit (Qiagen)
Using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (E6420L) and a normalized RNA input between 200pg-50ng a template switching method is used to generate cDNAs. The NEB Ultra II FS workflow is used for fragmentation, end repair, dA-tailing, adapter ligation and PCR. Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

value: peripheral blood

value: B lymphocytes


title: 9_ARC_pos


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S4_ATCACG


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S2_ACTTGA


title: 7E_M_413


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S1_GCCAAT


title: 7E_M_412


title: 7E_M_410


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S12_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S1_CGATGT


title: 7E_M_411


title: LOVO cells, spheroids

city: Dalian

first: Jiaojiao

last: Hao

address: No.9 West Section of Lvshun South Road, Dalian City, Liaoning Province, China

institute: Dalian Medical 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
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: LOVO

growth_protocol: HCT116 and LOVO cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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: LOVO

value: colon cancer cells


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S12_CGATGT

value: Cortex

value: 6-10 weeks


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S12_CTTGTA

value: Male

value: wild-type


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S11_TAGCTT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S11_GCCAAT


title: HCT116 cells, spheroids


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S12_CAGATC


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S1_TAGCTT


title: 7E_M_408


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S12_ACTTGA


title: 7E_M_409


title: HCT116 cells, adherent

value: NO


title: LOVO cells, adherent


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S11_CGATGT


title: 7E_M_407


title: B5_S83

city: Ramat Gan

first: Talia

last: Golan

state: <None>

address: Tel Hashomer

department: Oncology Institute

country: Israel

institute: Sheba Medical Center

data_processing:
STAR alignment, output sorted genomes.
XenofilteR on sorted genomes.
Unsort filtered bams to fastqs.
Realign filtered FASTQs with STAR,   output   unsorted transcriptome
RSEM on realigned bam.
Assembly: Create CPM matrix.
Supplementary files format and content: BRCA_CPM.csv - cvs file including CPM data for each sample

source_name: Human;PDX

growth_protocol: Tumor tissue from patient derived xenograft (PDX) was snaped frozen in liquie nitrogen

extract_protocol:
NucleoSpin® RNA, MACHEREY-NAGEL
Bulk MARS-seq

treatment_protocol: No treatment in vivo

value: PDAC

value: Patient derived xenofraft

value: BRCA

value: No


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S11_CAGATC


title: B5_S97


title: B5_S98


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S11_ACTTGA


title: 7E_M_406


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S10_GCCAAT


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S10_CTTGTA


title: B5_S71


title: 7E_M_405


title: B5_S63


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S10_ATCACG


title: snhmCseq_Brain1_NeuN_pos_nextseq07.03.2019_S10_ACTTGA


title: 7E_M_404


title: B5_S6


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S9_GCCAAT


title: B5_S55


title: 7E_M_402


title: 7E_M_401


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S9_CTTGTA


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S8_CTTGTA


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S8_CAGATC


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S8_CGATGT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S9_ACTTGA


title: 7E_M_400


title: B5_S49


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S8_GCCAAT


title: 7E_M_399


title: B5_S32


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S8_ATCACG


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S7_GCCAAT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S7_TAGCTT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S7_CGATGT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S7_CTTGTA


title: 7E_M_398


title: B5_S26


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S6_TGACCA


title: 7E_M_397


title: 7E_M_403


title: B5_S53


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S6_CAGATC


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S6_TAGCTT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S5_GCCAAT


title: B5_S21


title: B5_S46


title: B5_S19


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S5_CGATGT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S4_GCCAAT


title: B5_S160


title: 7E_M_396


title: 7E_M_395


title: 7E_M_393


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S4_CTTGTA


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S3_TAGCTT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S3_CTTGTA


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S4_ACTTGA


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S2_GCCAAT


title: B5_S151


title: B5_S149


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S5_ACTTGA


title: 7E_M_392


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S2_CAGATC


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S4_ATCACG


title: 7E_M_391


title: B5_S135


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S1_CTTGTA


title: 7E_M_390


title: B5_S127


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S1_CAGATC


title: 7E_M_389


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S12_GCCAAT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S12_TAGCTT


title: 7E_M_394


title: B5_S126


title: B5_S120


title: 7E_M_388


title: B5_S146


title: B5_S108


title: 7E_M_385


title: B5_S119


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S12_CGATGT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S12_CAGATC


title: 7E_M_386


title: B4_S92


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S12_ACTTGA


title: 7E_M_387


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S2_ACTTGA


title: B4_S87


title: 7E_M_383


title: B4_S81


title: 7E_M_384


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S12_ATCACG


title: 7E_M_254


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S11_CTTGTA


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S11_CGATGT


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S11_CAGATC


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S12_TGACCA


title: Tumor derived from KO+NM1 02

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
All of the subsequent analysis, including quality trimming, was executed using the BioSAILs workflow execution system. Trimmomatic (version 0.36) was used for quality trimming of the raw reads to get rid of low-quality bases, systematic base calling errors, as well sequencing adapter contamination (Bolger et al., 2014). The quality of the sequenced reads pre/post quality trimming was assessed by FastQC and only the reads that passed quality trimming in pairs were retained for downstream analysis (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The quality-trimmed RNA-Seq reads were aligned to the Mus musculus GRCm38 (mm10) genome using HISAT2 (version 2.0.4) (Kim et al., 2015). The conversion and sorting of SAM alignment files for each sequenced sample to BAM format was done by using SAMtools (version 0.1.19) (Li et al., 2009). The BAM alignment files were processed using HTseq-count, using the reference annotation file to produce raw counts for each sample.
Assembly: GRCm38 (mm10)
Supplementary files format and content: read counts

source_name: Tumor derived from KO+NM1

growth_protocol: Nuclear Myosin 1 Knock-Out (NM1 KO) cell lines were derived from wild-type mouse embryonic fibroblasts (MEFs) (ATCC® CRL-2752) (NM1 WT) using the CRISPR/Cas9 system (Venit et al., 2020). For the NM1 rescue experiment we transduced NM1 KO MEFs by lentiviral vector carrying coding sequence for NM1 fused with HA and V5 tag (Vectorbuilder). The cells expressing NM1-HA-V5 were selected by Neomycin and single clones tested by Western blot by specific anti-HA antibodies.  Cells were grown in a DMEM medium containing 10% fetal bovine serum, 100 U/ml penicillin, and 100 mg/ml streptomycin (Millipore-Sigma) in a humidified incubator with 5% CO2 at 37 °C. For tumor tissue preparation: A total of 15 female 16-week-old nude mice, 25-35 g in weight, were divided into two groups comprised of 5 mice per group. The mice were injected with NM1 WT, KO  and rescue KO+NM1 embryonic fibroblasts (0.1 mL, 3 x 10mil cells/100 µL in 10 mM PBS, pH 7.4) subcutaneously into the right flank of each nude mouse. Mice were weighed daily and monitored for mobility, respiratory distress, and signs of pain for up to 30 days. A weight loss of more than 20% was deemed to be unacceptable and would lead to early sacrifice of the mouse. The tumor size was measured by caliper in each mouse daily and at the end of 30 days cycle, all mice from each group were euthanized by CO2 exposure and perfused with isotonic PBS followed by rapid removal of tumors.

extract_protocol:
RNA from both tumors and cells were isolated by TRIreagent according to manufacturers' protocol.
For transcriptional profiling of tumor tissues, NM1 KO tumor and KO+NM1 tumor were divided to 4 equal pieces and each piece separately homogenized in RNAzol reagent by using the Bead Ruptor 96 Homogenizer (Omni International). Total RNA from 3 replicates of NM1 KO tumor and 4 replicates of KO+NM1 tumor was extracted according to the manufacturer’s protocol.The RNA-Seq library was prepared by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with the NextSeq 500/550 sequencing platform (performed at the NYUAD Sequencing Center).

value: Tumor

tag: protocol

value: NM1 KO with NM1 rescue


title: Tumor derived from NM1 KO 01

source_name: Tumor derived from NM1 KO

value: NM1 KO


title: Tumor derived from KO+NM1 01


title: Tumor derived from NM1 KO 02


title: Tumor derived from KO+NM1 03


title: Tumor derived from KO+NM1 04


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S12_CTTGTA


title: Tumor derived from NM1 KO 03


title: MMQ UNC 24h

city: Wuhan

first: Zhoubin

last: Tan

state: Hubei province

institute: Tongji Hospital, Wuhan, China

data_processing:
Basecalls are performed using CASAVA
Reads are aligned to the genome using the split read aligner TopHat (v2.0.7) and Bowtie2, using default parameters.
HTSeq is used for estimating their abundances.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Rat pituitary tumor cells

growth_protocol: MMQ cells were cultured in DMEM/F12 medium (Gibco, 31331093), supplemented with 2.5% fetal bovine serum (Gibco, 26140079) and 15% horse serum (BI, 04-124-1A).

extract_protocol:
Total RNAs from MMQ cells are isolated using TRIzol reagent (Invitrogen) and treated with RNase-free DNase I (New England Biolabs, MA, USA), to remove any contaminating genomic DNA. mRNA extraction is performed using Dynabeads oligo(dT) (Invitrogen Dynal).Double-stranded complementary DNAs are synthesized using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. The cDNAs are then fragmented by nebulization and the standard Illumina protocol is followed thereafter, to create the mRNA-seq library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MMQ cells were treated with UNC9994 (15μM) or vehicle control (DMSO) for 12h or 24h

value: MMQ (ATCC CRL-10609 TM) cells

value: treated with UNC9994 for 24h


title: 7E_M_253


title: B4_S73


title: MMQ UNC 12h

value: treated with UNC9994 for 12h


title: B4_S72


title: 7E_M_252


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S10_CTTGTA


title: B4_S70


title: MMQ Ctrl 12h

value: treated with DMSO for 12h


title: B4_S67


title: Mouse.cortex_NeuN.neg

description: Drop-seq

data_processing:
The computational data analysis of sNucDrop-seq was performed as previously described with minor modifications (Hu* & Fabyanic* et al., 2017; PMID: 29220646). Paired-end sequencing reads of sNucDrop-seq experiments were first processed using publicly available the Drop-Seq Tools v1.12 software. Briefly, each mRNA read (read2) was tagged with the cell barcode (bases 1 to 12 of read 1) and unique molecular identifier (UMI, bases 13 to 20 of read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned using STAR v 2.5.2a to the mouse (mm10, Gencode release vM13). The intronic reads were also retained for downstream analysis. A custom Perl script was implemented in the Drop-Seq Tools pipeline to retrieve both exonic and intronic reads mapped to predicted strands of annotated genes. Uniquely mapped reads were grouped by cell barcodes. Cell barcodes were corrected for possible bead synthesis errors, using the DetectBeadSynthesisErrors program from the Drop-Seq Tools v1.12 software. To generate digital expression matrix, a list of UMIs in each gene (as rows), within each nucleus (as columns), was assembled, and UMIs within ED = 1 were merged together. The total number of unique UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given nucleus.  After obtaining the digital expression matrices, emptyDrops function in R package DropletUtils (v1.2.2) was used to filter out the empty droplets. We used Scrublet (v0.2.1) with the expected_doublet_rate parameter of 0.05 to identify the doublets which were removed. Pass filter nuclei were identified with following QC parameters (nFeature_RNA > 500 & nFeature_RNA <= 3000 & percent.mt < 5) in Seurat (v3.2.3). Top 2,000 highly variable genes were identified. The expression level of highly variable genes was scaled and centered for each gene and was subjected to PCA. The top 30 PCs were selected and used for UMAP reduction in Seurat with the default parameters. Clusters were identified using the function FindClustes in Seurat with the resolution parameter set to 1. The marker genes were identified using FindAllMarkers in Seurat with the default parameters. The top-ranking markers of each cluster were used to annotate the clusters.
Assembly: mm10
Supplementary files format and content: gene expression matrix containing read counts for each gene (rows) in each cell/nucleus (columns)

molecule: polyA RNA

growth_protocol: All experiments were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) at the University of Pennsylvania. Mice were group-housed in cages of three to five in a 12-hr light/dark cycle with food and water provided ad libitum. All mice used for experiments were naïve to behavioral assays and other procedures. For all bulk-nucleus and single-nucleus experiments, 6-10 weeks old, wild-type, male mice in a pure C57BL/6J background were used. For prospectively isolating neuronal (NeuN-positive) and non-neuronal (NeuN-negative) nuclei to benchmark snhmC-seq and joint-snhmC-seq, 6-10 week-old wild-type mice from a C57BL/6J background were used as previously described (Johnson et al. 2017; PMID: 28920956).

extract_protocol:
Nuclei isolation from mouse cortical tissues was performed as described with minor modifications (Hu* & Fabyanic* et al., 2017; PMID: 29220646). Briefly, mouse brains were rapidly resected on ice. Cortices were flash-frozen in liquid nitrogen and stored at -80°C before nuclear isolation. Next, 14mL sucrose cushion (1.8M sucrose (Sigma-Aldrich, RNase and DNase free, ultra-pure grade), 10mM Tris-HCl pH 8.0, 3mM MgAc2 (Sigma-Aldrich), and protease inhibitor cocktail (Roche)) was added to the bottom of centrifuge tubes (Beckman Coulter). Using a glass homogenizer (Wheaton), a frozen mouse cortical sample was dounce homogenized (19 times with loose pestle followed by 4 times with tight pestle) in 12mL homogenization buffer (0.32M sucrose, 5mM CaCl2 (Sigma-Aldrich), 3mM MgAc2, 10mM Tris-HCl pH 8.0, 0.1% Triton X-100 (Sigma-Aldrich), 0.1mM EDTA (Invitrogen), protease inhibitor cocktail (Roche)). Homogenates (~12ml) were carefully layered onto the sucrose cushion in the centrifuge tubes, and 10mL homogenization buffer was added atop of the homogenates. The tubes were then balanced and centrifuged in a Beckman Coulter L7-65 Ultracentrifuge at 82,705 g at 4°C for 2hr using a Beckman Coulter SW28 swing bucket rotor (Beckman Coulter). The supernatant was carefully removed via aspiration. 1ml chilled DPBS was added to resuspend the nuclear pellet, and nuclei were subsequently transferred to a 1.5-mL tube. Nuclei were pelleted at 500 g for 10 min at 4C, and then resuspended in 0.01% BSA (Sigma-Aldrich) in DPBS. After resuspension, nuclei were filtered through a 40-μm cell strainer (Fisher Scientific), visually inspected for morphology and quality assurance, and counted using a Fuchs-Rosenthal counting chamber before FANS.
Drop-seq platform based single-nucleus RNA-sequencing (snRNA-seq/sNucDrop-seq) was performed as previously reported with some modifications related to NeuN antibody based nuclei isolation (Hu* & Fabyanic* et al., 2017; PMID: 29220646). Briefly, FANS-sorted NeuN-positive and NeuN-negative nuclei were individually diluted to a concentration of 100 nuclei/mL in DPBS containing 0.01% BSA. Approximately 1.25 mL of this single-nucleus suspension was loaded for each sNucDrop-seq run. The single-nucleus suspension was then co-encapsulated with barcoded beads (ChemGenes) using an Aquapel-coated PDMS microfluidic device (mFluidix) connected to syringe pumps (KD Scientific) via polyethylene tubing with an inner diameter of 0.38mm (Scientific Commodities). Barcoded beads were resuspended in lysis buffer (200 mM Tris-HCl pH8.0, 20 mM EDTA, 6% Ficoll PM-400 (GE Healthcare/Fisher Scientific), 0.2% Sarkosyl (Sigma-Aldrich), and 50 mM DTT (Fermentas; freshly made on the day of run) at a concentration of 120 beads/mL. The flow rates for nuclei and beads were set to 4,000 mL/hr, while QX200 droplet generation oil (Bio-rad) was run at 15,000 mL/hr. A typical run lasts 20 min. Droplet breakage with Perfluoro-1-octanol (Sigma-Aldrich), reverse transcription and exonuclease I treatment were performed, as previously described, with minor modifications7. For up to 120,000 beads, 200 μL of reverse transcription (RT) mix (1x Maxima RT buffer (ThermoFisher), 4% Ficoll PM-400, 1 mM dNTPs (Clontech), 1 U/mL RNase inhibitor, 2.5 mM Template Switch Oligo (TSO: AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG) (Macosko et al., 2015), and 10 U/ mL Maxima H Minus Reverse Transcriptase (ThermoFisher)) were added. The RT reaction was incubated at room temperature for 30min, followed by incubation at 42C for 120 min. To determine an optimal number of PCR cycles for amplification of cDNA, an aliquot of 6,000 beads was amplified by PCR in a volume of 50 μL (25 μL of 2x KAPA HiFi hotstart readymix (KAPA biosystems), 0.4 μL of 100 mM TSO-PCR primer (AAGCAGTGGTATCAACGCAGAGT (Macosko et al., 2015), 24.6 μL of nuclease-free water) with the following thermal cycling parameter (95C for 3 min; 4 cycles of 98C for 20 sec, 65C for 45 sec, 72C for 3 min; 9 cycles of 98C for 20 sec, 67C for 45 sec, 72C for 3 min; 72C for 5 min, hold at 4C). After two rounds of purification with 0.6x SPRISelect beads (Beckman Coulter), amplified cDNA was eluted with 10 μL of water. 10% of amplified cDNA was used to perform real-time PCR analysis (1 μL of purified cDNA, 0.2 μL of 25 mM TSO-PCR primer, 5 μL of 2x KAPA FAST qPCR readymix, and 3.8 μL of water) to determine the additional number of PCR cycles needed for optimal cDNA amplification (Applied Biosystems QuantStudio 7 Flex). We then prepared PCR reactions per total number of barcoded beads collected for each sNucDrop-seq run, using 6,000 beads per 50-μL PCR reaction, and ran the aforementioned program to amplify the cDNA for 4 + 10 to 12 cycles. We then tagmented cDNA using the Nextera XT DNA sample preparation kit (Illumina, FC-131-1096), starting with 550 pg of cDNA pooled in equal amounts, from all PCR reactions for a given run. Following cDNA tagmentation, we further amplified the tagmented cDNA libraries with 12 enrichment PCR cycles using the Illumina Nextera XT i7 primers along with the P5-TSO hybrid primer (AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGT*A*C) (Macosko et al., 2015). After quality control analysis by Qubit 3.0 (Invitrogen) and a Bioanalyzer (Agilent), libraries were sequenced on an Illumina NextSeq 500 instrument using the 75-cycle High Output v2 Kit (Illumina). We loaded the library at 2.0 pM and provided Custom Read1 Primer (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) at 0.3 mM in position 7 of the reagent cartridge. The sequencing configuration was 20 bp (Read1), 8 bp (Index1), and 60 bp (Read2).

tag: facs

value: NeuN-negative


title: 7E_M_249


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S10_CGATGT

value: Cortex


title: 7E_M_250


title: snhmCseq_Brain1_NeuN_neg_nextseq07.03.2019_S10_ACTTGA

value: 6-10 weeks


title: 7E_M_251


title: Mouse.cortex_NeuN.pos

description: Drop-seq

value: Male

value: NeuN-positive


title: 694-CD-AM

first: Yijun

last: Yang

address: 3500 North Broad St., MERB 1007

institute: Temple University School of Medicine

data_processing:
Raw data quality was evaluated with FastQC, reads were mapped onto Mus musculus GRCm38 reference genome with STAR aligner v2.5.2b.
Genome was available on ENSEMBL. BAM files were generated and used to extract unique gene hit counts using FeatureCounts from Subread package v.1.5.2.
Assembly: mm10
Supplementary files format and content: FeatureCounts output for each sample

extract_protocol:
extraction from tissue via Qiagen RNeasy kit, performed via manufacturer s instructions
libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's instructions

treatment_protocol: C57BL/6J female mice were fed a Western diet (WD, Research Diets, D12451, with 45%kcal fat and 17%kcal sucrose) for 15 weeks in order to induce an earlystage Metabolic syndrome (MetS) phenotype; mice fed a normal chow served as control (CD, Research Diets, D12450K, with 10% kcal fat). After 15 weeks of feeding, CD or WD treated mice were randomly subjected to breeding and induced pregnancy or maintained on the diet without breeding for the same duration. Pregnant mice were terminated 1 day after delivery (27-29 weeks old), nonpregnant mice were terminated at age of 27-29 weeks. At terminal, heart tissues were carefully trimmed and collected, then rinsed with PBS. Tissues were partially snap frozen in liquid nitrogen for molecular analysis

value: Heart

tag: gender

value: Female

value: WT

value: Control Diet

tag: time point

value: Age-matched non-pregnant


title: 7E_M_248

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2


title: 692-CD-AM

tag: tissue


title: B4_S77

value: PDAC

value: Patient derived xenofraft

value: BRCA

value: No


title: B4_S62


title: 7E_M_247


title: EpCAM Prox, rep2

city: Copenhagen N

first: Laura

middle: Maarit

last: Pikkupeura

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description:
E16_SI_prox_Epithelium_2
in_vivo_counts.tsv

data_processing:
Reads were aligned using qAlign function from Bioconductor package QuasR (Gaidatzis et al),with default parameters.
Mapped reads were assigned to known UCSC genes and  quantified with qCount function from QuasR.
DE analysis was carried out using edgeR with default settings unless otherwise noted.
Assembly: mm10
Supplementary files format and content: Gene counts for each sample as tab separated text file

source_name: Proximal E16.5 intestine

extract_protocol: RNA was collected using RNAeasy Microkit (Qiagen). The samples were sequenced with Illumina NextSeq.

value: Proximal E16.5 intestine


title: EpCAM Prox, rep3

description:
E16_SI_prox_Epithelium_3
in_vivo_counts.tsv


title: B4_S60


title: MMQ Ctrl 24h

tag: cell line

value: MMQ (ATCC CRL-10609 TM) cells

value: treated with DMSO for 24h


title: 7E_M_246

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: 689-WD-AM

value: Western Diet


title: B4_S57


title: EpCAM Prox, rep1

description:
E16_SI_prox_Epithelium_1
in_vivo_counts.tsv

tag: cell type


title: B4_S65

tag: treatment


title: 686-CD-AM


title: 7E_M_245


title: 7E_M_244


title: B4_S56


title: 685-WD-AM


title: B4_S51


title: Adult_SI_prox_Lin_neg_EpCAM_pos_CD24_med_Epithelium, rep2

description:
MM380
in_vivo_counts.tsv

data_processing:
Data was processed together with EpCAM+/DAPI-/CD31-/CD45- cells isolated from the proximal region of E16.5 intestine available in GSE183671
Reads were aligned using qAlign function from Bioconductor package QuasR (Gaidatzis et al),with default parameters.
Mapped reads were assigned to known UCSC genes and  quantified with qCount function from QuasR.
DE analysis was carried out using edgeR with default settings unless otherwise noted.
Assembly: mm10
Supplementary files format and content: Gene counts for each sample as tab separated text file

source_name: Proximal small intestine

growth_protocol: Crypts were isolated from the proximal 20% of the small intestine and and incubated with collagenase to obtain single cells. Following the exclusion of DAPI negative and lineage negative cells, EpCAM positive and CD24-mid expressing cells were purified using a FACSAria III cell sorter into RLT buffer.

treatment_protocol: RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-Seq v2 Pico Input Mammalian kit (Takara).

value: Proximal small intestine

value: Adult

value: Wildtype


title: 690-WD-AM


title: 682-CD-PP

value: Post-partum day 1


title: 7E_M_243


title: 7E_M_242


title: 681-CD-PP

value: Heart


title: FEnS, rep3

description:
33-FEnS-C
dox_counts.tsv

data_processing:
Data was processed together with doxycycline treated or untreated TetON-YAP-H2B-mCherry adult epithelial organoids
Mapping and quantification of fastq files were done via the Rsubread package. Reads were mapped to the mm10 genome assembly using the align-function with default settings.
Mapped reads were quantified across RefSeq gene models using the featureCounts-function with default settings.
DE analysis was carried out using edgeR with default settings unless otherwise noted.
Assembly: mm10
Supplementary files format and content: Gene counts for each sample as tab separated text file

growth_protocol: Epithelial fragments from fetal intestine (intestines from three fetuses were pooled for each sample) and scraped adult crypts (from one individual per sample) were harvested from the proximal parts of the small intestine using EDTA (2mM). Harvested epithelial fragments adult crypts were embedded in Matrigel droplets and cultured in advanced DMEM/F12 with GlutaMAX and Penicillin/Streptomycin supplemented with EGF (Peprotech; 50 ng/ml), Noggin (Peprotech; 100ng/mL), and R-spondin1 (R&D Systems; 500 ng/ml). When indicated, the growth medium was supplemented with CHIR99021 (Stemgent; 3μM) and Nicotinamide (Sigma; 10 mM).

treatment_protocol: Libraries were prepared using TruSeq RNA kit (Illumina) following manufacturer instructions.

value: Epithelial organoids

value: Control


title: 679-WD-PP

value: Female

value: WT


title: B4_S44

value: PDAC


title: B4_S47

value: Patient derived xenofraft


title: 7E_M_241


title: B4_S41

value: BRCA


title: FEnS, rep2

description:
32-FEnS-B
dox_counts.tsv


title: 678-WD-PP


title: 7E_M_240


title: Adult_SI_prox_Lin_neg_EpCAM_pos_CD24_med_Epithelium, rep3

description:
MM397
in_vivo_counts.tsv


title: B4_S38

value: No


title: 672-WD-PP


title: FEnS, rep1

description:
31-FEnS-A
dox_counts.tsv


title: B4_S36


title: 7E_M_239


title: plusDOX, rep3

description:
plusDOX-C
dox_counts.tsv

data_processing:
Mapping and quantification of fastq files were done via the Rsubread package. Reads were mapped to the mm10 genome assembly using the align-function with default settings.
Mapped reads were quantified across RefSeq gene models using the featureCounts-function with default settings.
DE analysis was carried out using edgeR with default settings unless otherwise noted.
Assembly: mm10
Supplementary files format and content: Gene counts for each sample as tab separated text file

value: Doxycyclin


title: 7E_M_238


title: 670-CD-PP

value: Control Diet


title: Adult_SI_prox_Lin_neg_EpCAM_pos_CD24_med_Epithelium, rep1

description:
MM366
in_vivo_counts.tsv


title: B4_S30


title: 7E_M_237


title: plusDOX, rep2

description:
plusDOX-B
dox_counts.tsv


title: B4_S28


title: 7E_M_236


title: B4_S24


title: B3_S93


title: 7E_M_235


title: IP-OG1-2

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

data_processing:
For raw data of ChIP-seq, trim_galore (version 0.4.4) (https://github.com/FelixKrueger/TrimGalore) was used to process the quality control. After that, the adapters, the reads with quality lower than 30 and length shorter than 50bp were filtered. The cleaned paired reads were mapped to TAIR10 genome reference using bowtie2 (version 2.2.9) with default parameters.The mapping files were filtered by samtools (version: 0.1.19) and grep command to keep the unique and high mapping quality reads. Furthermore, the PCR duplications were removed using samtools with parameter: rmdup.
The peaks were called using MACS2 (version 2.2.7.1) with parameters: --gsize 1.19e8 --qvalue 0.01. The Input samples were control. The coverage calculation of alignments was performed using bamCoverage from deepTools2 with parameters: --binSize=5 --normalizeUsing CPM.
Assembly: Tair10
Supplementary files format and content: bw text files include peak enrichment

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: seedlings grown in half-strength MS media

extract_protocol:
DNA samples were extracted by common methods
After the DNA sample was tested, the protein bound DNA fragments were specifically enriched by the technology of chromatin co-precipitation, and the whole library preparation was completed through the steps of terminal repair, adding A tail, adding sequencing connector, purification, PCR amplification, etc.

treatment_protocol: 11-day-old seedlings were treated with 10 mM MG132 for 7hrs

value: Total seedlings

value: ogdh double mutant


title: INPUT-OG1-2


title: INPUT-OG1-1


title: 7E_M_234

last: Ecker

institute: HHMI-Salk-Institute


title: B3_S66


title: minusDOX, rep1

description:
minusDOX-A
dox_counts.tsv

value: Proximal small intestine


title: Shoot 20 μM Phosphorus (severe stress), Replicate 3

city: Invergowrie / Dundee

first: Raul

last: Huertas

state: Perth and Kinross

address: Errol Road

department: Environmental and Biochemical Sciences

country: United Kingdom

institute: The James Hutton Institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence and mapped using to reference genome (v4.1) using HISAT2 2.0.5 and Stringtie 1.2.4 using default parameters.
Read count extraction and normalization were performed using Cuffdiff software.
Assembly: Panicum virgatum v4.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Panicum virgatum

source_name: Shoot

growth_protocol: Germinated seedling were growth in cones (6.9 cm in diameter X 25.4 cm in depth) filled with 40% all-purpose sand, 40% Q-ROK silica sand and 20% fine (2-4 mm particle size) perlite.

extract_protocol:
Total RNA was extracted using a cetyltrimethylammonium bromide (CTAB) and LiCl method (Chang, Puryear, & Cairney, 1993). RNA was treated with DNase I to remove genomic DNA.
RNA libraries were prepared using Illumina TruSeq RNA library preparation kit following manufacturer's protocols

treatment_protocol: Plants were watered daily to field capacity during a 4-week growth period with a modified nutrient solutions

value: Shoot

value: WT cv. Alamo

value: Pi limitation (severe)


title: Mouse_HOMER_LV_4

description: FACS-purfied left ventricular non-cardiomyocytes

data_processing:
10X Genomics Cell Ranger ( version 3.0.2) was used to demultiplex raw base call files from the Illumina sequencer to produce fastq files.
Cell Ranger was used to align the reads, filter out background-associated-barcodes, count barcodes and UMIs, and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: Count matrices in Market Exchange Format for sparse matrices and gzipped tsv files for genes and barcodes corresponding to row and column indices of the count matrices

source_name: left vetricular tissue

extract_protocol:
Viable (DAPI-), metabolically active (Calcein+), nucleated (VDR+), single cells were FACS-purified from digested left ventricular tissues, and subsequently loaded on a 10X Genomics Chromium Single Cell B chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics). Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR, and subsequently sequenced on an Illumina NextSeq 500 in high-output mode.

tag: Sex

value: male

value: left vetricular tissue

value: non-cardiomyocytes

tag: group

value: HOMER


title: B3_S31

tag: genotype


title: B3_S22


title: 7E_M_232

city: La Jolla

first: Joseph

address: 10010 North Torrey Pines Road

tag: brain region


title: Shoot 20 μM Phosphorus (severe stress), Replicate 2


title: Mouse_HOMER_LV_3


title: Shoot 20 μM Phosphorus (severe stress), Replicate 1


title: B3_S21


title: 7E_M_231

tag: age


title: Mouse_HOMER_LV_2


title: 7E_M_230

tag: strain


title: plusDOX, rep1

description:
plusDOX-A
dox_counts.tsv

value: Epithelial organoids


title: minusDOX, rep3

description:
minusDOX-C
dox_counts.tsv

value: Control


title: IP-OG1-1


title: B3_S103

value: PDAC

value: Patient derived xenofraft


title: 7E_M_228


title: Mouse_HOMER_LV_1


title: B3_S100

value: BRCA

value: No


title: minusDOX, rep2

description:
minusDOX-B
dox_counts.tsv


title: Shoot 60 μM Phosphorus (moderate stress), Replicate 2

value: Pi limitation (moderate)


title: 7E_M_227


title: B2_S46


title: Shoot 60 μM Phosphorus (moderate stress), Replicate 1


title: Mouse_sham_LV_4

value: sham


title: Shoot 200 μM Phosphorus (mild stress), Replicate 3

value: Pi limitation (mild)


title: 7E_M_233


title: Mouse_sham_LV_3


title: 7E_M_225


title: Mouse_sham_LV_2


title: Shoot 200 μM Phosphorus (mild stress), Replicate 2


title: B2_S38


title: 7E_M_224


title: B2_S37


title: Shoot 200 μM Phosphorus (mild stress), Replicate 1


title: Shoot 60 μM Phosphorus (moderate stress), Replicate 3


title: Shoot Control, Replicate 3

value: Optimal nutrition


title: B2_S36


title: RNA_Smarcc1 #2

description:
RNA-seq
counts.txt
Smarcc1_2_S15

data_processing:
After download of the base-called and demultiplexed reads from BaseSpace, the single-end 76 bp raw reads were quality assessed with FastQC (v0.11.7) and Fastq Screen (v0.11.4) and afterwards trimmed using Trimmomatic v0.32[43]. The trimmed reads were aligned to the mouse genome (mm10 assembly excluding non-canonical chromomes) using STAR[44] (v2.7.3a) in two-pass mode and guided by a RefSeq gene annotation.
Bam file indices were created using samtools[45] (v1.10). The mapped reads were assigned to genes with featureCounts[46] generating a count table.
Assembly: mm10
Supplementary files format and content: A tab delimited text file containing a matrix of sgRNA read counts in T0 and the three populations CD117+, CD117NegSca1Neg, and CD117NegSca1High in T1, T2, and T3

source_name: E16.5 fetal proximal small intestine

growth_protocol: Standard 3D Matrigel culture of organoids. ENR medium: adv.DMEM/F12, GlutaMAX, Hepes, Pencillin/Streptomycin (all from Thermo Fisher), EGF (Peprotech; 50 ng/mL), Noggin (Peprotech; 100 ng/mL) and conditioned R-spondin1 media (10%)

extract_protocol:
RNA was isolated from organoids using RNeasy Micro Kit (Qiagen).
RNA-seq libraries were generated with the TruSeq RNA Library Prep Kit (Illumina). The concentration and quality of the library was measured using Qubit and Bioanalyzer. The library was diluted to 2 nM and a final concentration of 1.7 pM was sequenced with Illumina High Output 75 cycles kit on an Illumina NextSeq 500 sequencer

value: E16.5 fetal proximal small intestine

value: Cas9-blasticidin plasmid transduced WT organoids transduced with Smarcc1 sgRNA

value: Untreated, 5 days in culture


title: B2_S42


title: B2_S34


title: 7E_M_226


title: RNA_Smarca4 #2

description:
RNA-seq
counts.txt
Smarca4_3_S11

value: Cas9-blasticidin plasmid transduced WT organoids transduced with smarca4 sgRNA


title: Shoot Control, Replicate 1

value: Shoot

value: WT cv. Alamo


title: RNA_Smarcc1 #1

description:
RNA-seq
counts.txt
Smarcc1_1_S2

value: Cas9-blasticidin plasmid transduced WT organoids transduced with scramble sgRNA


title: Shoot Control, Replicate 2


title: RNA_Smarca4 #1

description:
RNA-seq
counts.txt
Smarca4_2_S4

value: Epithelial organoids


title: 7E_M_222


title: B2_S32


title: 7E_M_220


title: 7E_M_219


title: B2_S31


title: Root 20 μM Phosphorus (severe stress), Replicate 2

source_name: Root

value: Root

value: Pi limitation (severe)


title: RNA_Neg2_ctrl 2

description:
RNA-seq
counts.txt
Neg2_2_high_S16

value: Cas9-blasticidin plasmid transduced WT organoids transduced with scrambled sgRNA


title: 7E_M_221


title: RNA_Neg2-ctrl 1

description:
RNA-seq
counts.txt
Neg2_RNA_1_high_S5


title: B2_S30

value: PDAC

value: Patient derived xenofraft

value: BRCA


title: 7E_M_218


title: Root 20 μM Phosphorus (severe stress), Replicate 1


title: B2_S29

value: No


title: Root 60 μM Phosphorus (moderate stress), Replicate 3

value: Pi limitation (moderate)


title: 7E_M_217


title: Root 60 μM Phosphorus (moderate stress), Replicate 2


title: ATAC_Smarcc1 #1

description:
ATAC-seq
Enh_ATAC_counts.txt
Smarcc1_1_low_S9

data_processing:
The NextSeq bcl format sequence data was downloaded from BaseSpace and using Illumina's blc2fastq (v2.20.0.422) base-called and demultiplexed. The raw 76 bp paired-end (PE) reads were first trimmed for Nextera transposase adapter sequences using Trimmomatic in palindrome mode. FastQC (v0.11.7) of reads before and after trimming confirmed the removal of any 3’-end adapter sequences, while also clearly showing the known insertion Tn5 motif in the 5’-end. FastQ Screen (v0.11.4) was furthermore used to check for sample contamination. The trimmed PE reads were mapped to the mouse genomes (mm10 assembly, canonical chromosomes only) using bowtie2 v.2.2.9 with default settings except -k 2 -X 2000 --no-mixed --no- discordant and finally converted to bam format using samtools (v1.10).  After sorting (SortSam) and labeling duplicates (MarkDuplicates) with Picard tools and adding a NH tag (number of reported alignments), reads were filtered to exclude unmapped, multimapping, and mitochondrial reads (samtools view -f 2 -F 4 and custom filter). The filtered bam files were converted to bed format using bedtools bamtobed.
Mapped reads were imported from bed files as ‘Datasets’ into EaSeq[50] (v. 1.2, http://easeq. net) for subsequent analysis using its integrated tools and default settings where nothing else is stated. A list of previously identified organoid enhancers including values from differential accessibility analysis as previously described (Pikkupeura and Bardini Bressan et al, 2022, submitted) was imported as a ‘Regionset’. ATAC-seq signal was quantified in 1 kbp windows centred at the previously identified regions using the ‘Quantify’ tool with all normalization disabled to give raw read-counts and the Regionset was exported. Based on this, a subset of regions was filtered having a signal above the 0.9 fractile in at least two of eight samples (two replicates of Smarca4, two replicates of Smarcc1, and four replicates of negative controls) and termed ‘filtered enhancers’.
Assembly: mm10
Supplementary files format and content: A tab delimited text file containing a matrix of sgRNA read counts in T0 and the three populations CD117+, CD117NegSca1Neg, and CD117NegSca1High in T1, T2, and T3

extract_protocol:
Organoids were isolated and dissociated to single cells and 50,000 live cells were sorted in 200 mL 0.1% BSA/PBS for generation of ATAC-seq libraries. Briefly, sorted cells were lysed and incubated with Tn5 Transposase (Illumina) for 30 minutes at 37C for DNA tagmentation
The tagged DNA was PCR amplified with sequence-compatible and barcoded primers for a total of 13 cycles. The concentration and quality of the libraries was analysed with Qubit and Bioanalyzer. The libraries were diluted to 2 nM in EB buffer and a final dilution of 1.5 pM was sequenced with Illumina High Output 150 pair-end  cycles kit on an Illumina NextSeq 500 sequencer.


title: Root 20 μM Phosphorus (severe stress), Replicate 3


title: 7E_M_216


title: B2_S27


title: Root 60 μM Phosphorus (moderate stress), Replicate 1


title: 7E_M_215


title: ATAC_Smarca4 #2

description:
ATAC-seq
Enh_ATAC_counts.txt
Smarca4_2_low_S8


title: ATAC_Smarca4 #1

description:
ATAC-seq
Enh_ATAC_counts.txt
Smarca4_1_low_S7


title: B2_S22


title: B2_S26


title: 7E_M_214


title: Root 200 μM Phosphorus (mild stress), Replicate 3

value: Pi limitation (mild)


title: 7E_M_213


title: B2_S21


title: ATAC_Neg2-ctrl high 1

description:
ATAC-seq
Enh_ATAC_counts.txt
Neg2_1_high_S5

value: E16.5 fetal proximal small intestine


title: Root 200 μM Phosphorus (mild stress), Replicate 1


title: ATAC_Neg2-ctrl_low 2

description:
ATAC-seq
Enh_ATAC_counts.txt
Neg2_2_low_S4


title: 7E_M_212


title: B2_S19


title: Root Control, Replicate 3

value: Optimal nutrition


title: ATAC_Smarcc1 #2

description:
ATAC-seq
Enh_ATAC_counts.txt
Smarcc1_2_low_S10

value: Cas9-blasticidin plasmid transduced WT organoids transduced with Smarcc1 sgRNA

value: Untreated, 5 days in culture


title: ATAC_Neg2-ctrl_low 1

description:
ATAC-seq
Enh_ATAC_counts.txt
Neg2_1_low_S3