title: Testis5

data_processing:
The drop-seq core computational tool was used for preprocessing of the Microwell-seq data. The implementation is described in the Drop-seq computational cookbook (http://mccarrolllab.org/dropseq/).
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: http://dec2017.archive.ensembl.org/Danio_rerio/Info/Index
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.


title: Liver5

status: Public on Nov 22 2021

type: SRA

city: Hangzhou

first: Mengmeng

last: Jiang

address: Yuhangtang Road 866, Xihu Distric

country: China

institute: Zhejiang University

library_source: transcriptomic

molecule: total RNA

organism: Danio rerio

source_name: liver

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: strain

value: Tubingen

tag: genotype

value: wild type

tag: tissue

value: liver


title: Ovary3

source_name: ovary

value: ovary


title: Testis1

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Danio rerio GRCz10
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

source_name: testis

tag: genotype/variation

value: testis


title: Kidney3

source_name: kidney

value: kidney


title: Intestine5

source_name: intestinePancreas

value: intestinePancreas


title: Heart5

source_name: heart

value: heart


title: Eye2

source_name: eye

value: eye


title: Spleen3

source_name: spleen

value: spleen


title: CaudalFin2

source_name: caudal fin

value: caudal fin


title: CaudalFin1


title: IFNgamma_rep2

status: Public on Nov 18 2021

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

country: USA

institute: University of Chicago

description: HeLa cells (ATCC) were cultured in the presence of 500 U/mL human interferon gamma (Peprotech) for 24 hours. RNA were extracted via the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol. PolyA+ RNA from 50 µg total RNA of each sample was extracted by Promega PolyATtract® mRNA Isolation Systems Z5313.

data_processing:
Library strategy: Nanopore direct RNA sequencing
base called by guppy base caller (version 3.2.2+9fe0a78) with min_qscore 7
aligned to by minimap2 (version 2.18-r1015) with parameters -ax splice -uf -k14
reads were piled up by samtools-v1.9
Genome_build: hg38 (Samples 1-6). rfam family RF02541, RF00177, human (NCBI: NR_003286.4, NR_003287.4), yeast (RNACentral: URS00005F2C2D_559292, URS000061F377_4932), C. elegans (RNACentral: URS00005A42AA_6239, URS00008C9AB9_6239), and Drosophila (RNACentral: URS000030AF9A_7227, URS000008C6A9_7227) (Sample 7).
Supplementary_files_format_and_content: csv files containing gene expression levels
Supplementary_files_format_and_content: csv files containing rRNA feature values used for model training
Supplementary_files_format_and_content: csv files containing psU predicted probabilities by model 3.0

molecule: polyA RNA

organism: Homo sapiens

source_name: HeLa cells polyA RNA

extract_protocol: The library preparation followed the protocol of Direct RNA Sequencing Kit (SQK-RNA002) provided by Oxford Nanopore Technology. Briefly, ~500 ng of Poly(A)+ RNA sample was used for each run. Each single run contained one biological replicate of one sample. The RT Adaptor (RTA) was ligated to the 3’ end of Poly(A)+ RNA by T4 DNA ligase (NEB M0202S) and then reverse transcribed by SuperScript III Reverse Transcriptase (ThermoFisher 12574018). The RNA was purified by 1.8x RNAClean XP beads (72 µL) (Beckman Coulter A63987) and then the RNA Adaptor (RMX) was ligated to the 3’ end of Poly(A)+ RNA using T4 DNA ligase (NEB M0202S) and then the RNA was purified with 1x RNAClean XP beads (40 µL). The sample was eluted with 21 µl Elution Buffer. Then the sample was loaded onto a R9.4.1 flow cell (FLO-MIN106D) in a MinION sequencer. Each flow cell was sequenced for 72 hours.

tag: treatment

value: treated with IFN gamma for 24h

tag: cell line

value: HeLa cells (ATCC)


title: IFNbeta_rep2

description: HeLa cells (ATCC) were cultured in the presence of 500 U/mL human interferon beta (Peprotech) for 24 hours. RNA were extracted via the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol. PolyA+ RNA from 50 µg total RNA of each sample was extracted by Promega PolyATtract® mRNA Isolation Systems Z5315.

value: treated with IFN beta for 24h


title: untreated_rep1

description: HeLa cells (ATCC) were incubated for 24 hours without treatment. RNA were extracted via the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol. PolyA+ RNA from 50 µg total RNA of each sample was extracted by Promega PolyATtract® mRNA Isolation Systems Z5310.

value: untreated


title: untreated_rep2

description: HeLa cells (ATCC) were incubated for 24 hours without treatment. RNA were extracted via the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol. PolyA+ RNA from 50 µg total RNA of each sample was extracted by Promega PolyATtract® mRNA Isolation Systems Z5311.


title: rRNA_mixture_nanopore

description:
The total RNA is first size selected to remove RNA<200nt with ZYMO RNA Clean & Concentrator-5 (R1013) kit. Then it's polyadenylated by yeast Poly(A) Polymerase (ThermoFisher 74225Z25KU). Then another ronud of size selection is performed with ZYMO RNA Clean & Concentrator-5 (R1013) kit and RNA molecules >200nt were retained.
Homo sapiens, Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, microbiome

organism:
Saccharomyces cerevisiae
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
human feces metagenome

source_name: mixture of RNA >200nt from human, yeast, C.elegans, Drosophila and stool microbiome

value: Homo sapiens HEK293T cells, Saccharomyces cerevisiae BY4741 strain, Drosophila melanogaster S2 cells, Caenorhabditis elegans whole animal, human stool microbiome


title: rRNA_mixture_Illumina

description: Homo sapiens, Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, microbiome

data_processing:
Only read 2 from paired-end reads were mapped with bowtie2 (version: bowtie2-2.3.3.1-linux-x86_64) using the following parameters: bowtie2 -x $reference -U $read2   -S $ouput -q -p 10 --local --no-unal .
Bowtie2 output “sam” files were converted to sorted bam files with samtools
IGV was used to calculte mutations and stop rates with the following parameters: igvtools count -z 5 -w 1 -e 250 --bases $input $output $reference
Genome_build: rfam family RF02541, RF00177, human (NCBI: NR_003286.4, NR_003287.4), yeast (RNACentral: URS00005F2C2D_559292, URS000061F377_4932), C. elegans (RNACentral: URS00005A42AA_6239, URS00008C9AB9_6239), and Drosophila (RNACentral: URS000030AF9A_7227, URS000008C6A9_7227).
Supplementary_files_format_and_content: tsv files containing mutation rate of each site

extract_protocol:
The total RNA is first size selected to remove RNA<200nt with ZYMO RNA Clean & Concentrator-5 (R1013) kit. The sample was performed bisulfite treatment as described previously (PMID: 30872485).
Standard Illumina seq protocols


title: IFNgamma_rep1

description: HeLa cells (ATCC) were cultured in the presence of 500 U/mL human interferon gamma (Peprotech) for 24 hours. RNA were extracted via the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol. PolyA+ RNA from 50 µg total RNA of each sample was extracted by Promega PolyATtract® mRNA Isolation Systems Z5312.


title: Skin4

source_name: skin

value: skin


title: IFNbeta_rep1

description: HeLa cells (ATCC) were cultured in the presence of 500 U/mL human interferon beta (Peprotech) for 24 hours. RNA were extracted via the RNeasy Mini kit (Qiagen) following the manufacturer’s protocol. PolyA+ RNA from 50 µg total RNA of each sample was extracted by Promega PolyATtract® mRNA Isolation Systems Z5314.


title: control knockdown (GFP) in mature worker - rep 4

status: Public on Nov 04 2021

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
Reads were demultiplexed using bcl2fastq2 (Illumina) with the options “--mask-short-adapter-reads 20 --minimum-trimmed-read-length 20 --no-lane-splitting --barcode-mismatches 0”. Reads were aligned to the H. saltator v8.5 assembly (Shields et al., 2018) using STAR (Dobin et al., 2013). STAR alignments were performed in two passes, with the first using the options “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 7 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.07 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 250000”, and the second using the options “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 500000 --alignMatesGapMax 500000 --sjdbFileChrStartEnd [SJ_files]” where “[SJ_files]” corresponds to the splice junctions produced from all first pass runs.
Gene-level read counts were produced using featureCounts (Liao et al., 2014) with the options “-O -M --fraction -s 2 –p”, against a custom adapted NCBI Harpegnathos annotation (see following paragraph) using gene-level values (not individual mRNAs). Resulting counts were rounded to integers prior to importing into R for DESeq2 analysis in order to account for fractional count values associated with fractional counting of multi-mapping reads.
Genome_build: v8.5
Supplementary_files_format_and_content: Output of DESeq2 showing baseMean, logfoldchange, raw P-value, and adjusted P-value for three comparisons: Kr-h1i vs. GFPi in workeers; Kr-h1i vs. GFPi in gamergates; and worker vs. gamergate control (GFPi) ovaries -- 12 columns total plus one column for the geneIDs

organism: Harpegnathos saltator

source_name: ovaries

growth_protocol: Animals were housed in a plaster nest in a clean, temperature  (25°C) and humidity (50%) controlled ant facility on a 12-hour light/dark cycle and fed three times per week with live crickets.

extract_protocol:
Harpegnathos ovaries were dissected from single individuals, snap-frozen and then homogenized in TRIzol (Thermo Fisher Scientific, MA). RNA was purified and its quality visualized on agarose-formaldehyde gels.
For library preparation, polyA+ RNA was isolated from total RNA using Dynabeads Oligo(dT)25 (Thermo Fisher) and constructed into strand-specific libraries using the dUTP method (Parkhomchuk et al., 2009). UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics, MA), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual- indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter, CA) and quantified by qPCR after amplification.

treatment_protocol: Each ant was injected with a calibrated glass capillary needle directly into the head, right below the antennas with dicer-substrate siRNAs against Kr-h1 or GRP (control) dissolved in 5% glucose and mixed with the in vivo-jetPEI transfection reagent. 24 hours after the injections, the ovaries were dissected in neurobasal medium and processed for RNA extraction.

tag: caste

value: mature worker

tag: knockdown

value: GFP


title: Kr-h1 knockdown in mature worker - rep 2


title: Kr-h1 knockdown in mature worker - rep 3


title: Kr-h1 knockdown in mature worker - rep 1


title: control knockdown (GFP) in mature worker - rep 5


title: Kr-h1 knockdown in mature worker - rep 4


title: control knockdown (GFP) in mature worker - rep 3


title: control knockdown (GFP) in mature worker - rep 2


title: control knockdown (GFP) in mature worker - rep 1


title: Kr-h1 knockdown in mature gamergate - rep 7

value: mature gamergate


title: Kr-h1 knockdown in mature gamergate - rep 6


title: Kr-h1 knockdown in mature gamergate - rep 5


title: Kr-h1 knockdown in mature gamergate - rep 1


title: Kr-h1 knockdown in mature gamergate - rep 4


title: Kr-h1 knockdown in mature gamergate - rep 3


title: Kr-h1 knockdown in mature gamergate - rep 2


title: control knockdown (GFP) in mature gamergate - rep 4


title: control knockdown (GFP) in mature gamergate - rep 5


title: control knockdown (GFP) in mature gamergate - rep 3


title: control knockdown (GFP) in mature gamergate - rep 2


title: control knockdown (GFP) in mature gamergate - rep 1


title: input chromatin - worker - rep 1

description:
input.worker.rep1
internal reference:
XKRH1_Input_W_CB_b1

library_source: genomic

data_processing:
Reads were demultiplexed using bcl2fastq2 (Illumina) with the options “--mask-short-adapter-reads 20 --minimum-trimmed-read-length 20 --no-lane-splitting --barcode-mismatches 0”. Reads were trimmed using TRIMMOMATIC (Bolger et al., 2014) with the options “ILLUMINACLIP:[adapter.fa]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:15”, and aligned to the Harpegnathos v8.5 assembly (Shields et al., 2018) using bowtie2 v2.2.6 (Langmead et al., 2019) with the option “--sensitive-local”. Alignments with a mapping quality below 5 (using samtools) and duplicated reads were removed
peaks were called using macs2 v2.1.1.20160309 (Zhang et al., 2008) with the options “--call-summits –nomodel –B”.
Genome_build: v8.5
Supplementary_files_format_and_content: bed file containing consensus peaks for Kr-h1

molecule: genomic DNA

source_name: central brain

extract_protocol:
samples were crosslinked for 5 minutes followed by 12 minutes of sonication in a covaris S220.  Lysate was then clarified followed by overnight IP for Kr-h1.  10% of lysate was saved and prepared as sonication control libraries.
Libraries for sequencing were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645), as described by the manufacturer but using half volumes of all reagents and starting material. For PCR amplification optimal number of PCR cycles was determined using a qPCR side-reaction using 10% of adapter-ligated, size-selected DNA. 13 cycles of PCR were used for Kr-h1 libraries and 5 cycles were used for Input controls.

treatment_protocol: To induce worker–gamergate transitions 25 callow females (5 days old) were isolated from their original colonies and transferred with 3 males to a new nest without queens or gamergates. Every ant was individually painted with a unique two-color combination. Ants were carefully observed for 1–2 hours every morning and evening in the following two weeks to monitor dueling activities. The intermediate transition time points were collected on day 10 and 20 after isolation. After 100 days, all ants were scored for hunting behavior every other day. At 120 days after isolation the whole colony was sacrificed and the gamergate status was determined based on the presence of mature oocytes.

value: central brain

value: worker

tag: antibody

value: input

tag: antibody lot


title: Kr-h1 ChIP - gamergate - rep 2

description:
krh1.gamergate.rep2
internal reference:
XKRH1_Krh1_GG_CB_b2

value: gamergate

value: custom


title: input chromatin - worker - rep 3

description:
input.worker.rep3
internal reference:
XKRH1_Input_W_CB_b3


title: Kr-h1 ChIP - worker - rep 1

description:
krh1.worker.rep1
internal reference:
XKRH1_Krh1_W_CB_b1


title: Kr-h1 ChIP - gamergate - rep 3

description:
krh1.gamergate.rep3
internal reference:
XKRH1_Krh1_GG_CB_b3


title: Kr-h1 ChIP - worker - rep 2

description:
krh1.worker.rep2
internal reference:
XKRH1_Krh1_W_CB_b2


title: Kr-h1 ChIP - worker - rep 3

description:
krh1.worker.rep3
internal reference:
XKRH1_Krh1_W_CB_b3


title: control knockdown (GFP) in mature gamergate - rep 6


title: Kr-h1 knockdown in d10 gamergate - rep 4

description:
gamergate.Krh1i.rep4
internal reference:
200508.H5H5HBGXF.b0210
KRKD_Krh1i_10h_DU_exp2_b4

data_processing:
Reads were demultiplexed using bcl2fastq2 (Illumina) with the options “--mask-short-adapter-reads 20 --minimum-trimmed-read-length 20 --no-lane-splitting --barcode-mismatches 0”. Reads were aligned to the H. saltator v8.5 assembly (Shields et al., 2018) using STAR (Dobin et al., 2013). STAR alignments were performed in two passes, with the first using the options “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 7 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.07 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 250000”, and the second using the options “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 500000 --alignMatesGapMax 500000 --sjdbFileChrStartEnd [SJ_files]” where “[SJ_files]” corresponds to the splice junctions produced from all first pass runs.
Gene-level read counts were produced using featureCounts (Liao et al., 2014) with the options “-O -M --fraction -s 2 –p”, against a custom adapted NCBI Harpegnathos annotation (see following paragraph) using gene-level values (not individual mRNAs). Resulting counts were rounded to integers prior to importing into R for DESeq2 analysis in order to account for fractional count values associated with fractional counting of multi-mapping reads.
Genome_build: v8.5
Supplementary_files_format_and_content: matrix of per-sample normalized FPKM values for all protein-coding genes in the Hsalt NCBI annotation (release 102)

extract_protocol:
Harpegnathos central brains were dissected from single individuals, snap-frozen and then homogenized in TRIzol (Thermo Fisher Scientific, MA). RNA was purified and its quality visualized on agarose-formaldehyde gels. Typical yields amounted to 0.6 µg total RNA per central brain.
For library preparation, polyA+ RNA was isolated from 600 ng total RNA using Dynabeads Oligo(dT)25 (Thermo Fisher) and constructed into strand-specific libraries using the dUTP method (Parkhomchuk et al., 2009). UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics, MA), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual- indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter, CA) and quantified by qPCR after amplification.

treatment_protocol: Each ant was injected with a calibrated glass capillary needle directly into the head, right below the antennas with dicer-substrate siRNAs against Kr-h1 or GRP (control) dissolved in 5% glucose and mixed with the in vivo-jetPEI transfection reagent. 10 hours after the injections, the central brain was dissected in neurobasal medium, and processed for RNA extraction.

value: d10 gamergate (dueler)


title: input chromatin - gamergate - rep 2

description:
input.gamergate.rep2
internal reference:
XKRH1_Input_GG_CB_b2


title: Kr-h1 knockdown in d10 gamergate - rep 5

description:
gamergate.Krh1i.rep5
internal reference:
200626.HCF2WBGXF.ND10
KRKD_Krh1i_10h_DU_exp3_b5


title: Kr-h1 knockdown in d10 gamergate - rep 6

description:
gamergate.Krh1i.rep6
internal reference:
200626.HCF2WBGXF.ND19
KRKD_Krh1i_10h_DU_exp3_b6


title: Kr-h1 knockdown in d10 gamergate - rep 7

description:
gamergate.Krh1i.rep7
internal reference:
200626.HCF2WBGXF.ND37
KRKD_Krh1i_10h_DU_exp3_b7


title: Kr-h1 knockdown in d10 gamergate - rep 8

description:
gamergate.Krh1i.rep8
internal reference:
200626.HCF2WBGXF.ND55
KRKD_Krh1i_10h_DU_exp3_b8


title: input chromatin - worker - rep 2

description:
input.worker.rep2
internal reference:
XKRH1_Input_W_CB_b2


title: Kr-h1 knockdown in d10 worker - rep 5

description:
worker.Krh1i.rep5
internal reference:
200626.HCF2WBGXF.ND01
KRKD_Krh1i_10h_CW_exp3_b5

value: d10 worker


title: Kr-h1 knockdown in d10 gamergate - rep 2

description:
gamergate.Krh1i.rep2
internal reference:
200508.H5H5HBGXF.H208
KRKD_Krh1i_10h_DU_exp2_b2


title: Kr-h1 knockdown in d10 worker - rep 6

description:
worker.Krh1i.rep6
internal reference:
200626.HCF2WBGXF.ND28
KRKD_Krh1i_10h_CW_exp3_b6


title: Kr-h1 knockdown in d10 gamergate - rep 1

description:
gamergate.Krh1i.rep1
internal reference:
200508.H5H5HBGXF.H181
KRKD_Krh1i_10h_DU_exp2_b1


title: Kr-h1 knockdown in d10 gamergate - rep 3

description:
gamergate.Krh1i.rep3
internal reference:
200508.H5H5HBGXF.b0109
KRKD_Krh1i_10h_DU_exp2_b3


title: input chromatin - gamergate - rep 1

description:
input.gamergate.rep1
internal reference:
XKRH1_Input_GG_CB_b1


title: Kr-h1 knockdown in d10 worker - rep 7

description:
worker.Krh1i.rep7
internal reference:
200626.HCF2WBGXF.ND46
KRKD_Krh1i_10h_CW_exp3_b7


title: Kr-h1 knockdown in d10 worker - rep 4

description:
worker.Krh1i.rep4
internal reference:
200626.HCF2WBGXF.b0505
KRKD_Krh1i_10h_CW_exp2_b4


title: Kr-h1 knockdown in d10 worker - rep 3

description:
worker.Krh1i.rep3
internal reference:
200626.HCF2WBGXF.b0404
KRKD_Krh1i_10h_CW_exp2_b3


title: Kr-h1 knockdown in d10 worker - rep 1

description:
worker.Krh1i.rep1
internal reference:
200626.HCF2WBGXF.b0202
KRKD_Krh1i_10h_CW_exp2_b1


title: Kr-h1 ChIP - gamergate - rep 1

description:
krh1.gamergate.rep1
internal reference:
XKRH1_Krh1_GG_CB_b1


title: Kr-h1 knockdown in d10 worker - rep 2

description:
worker.Krh1i.rep2
internal reference:
200626.HCF2WBGXF.b0303
KRKD_Krh1i_10h_CW_exp2_b2


title: input chromatin - gamergate - rep 3

description:
input.gamergate.rep3
internal reference:
XKRH1_Input_GG_CB_b3


title: control knockdown (GFP) in d10 gamergate - rep 8

description:
gamergate.GFPi.rep8
internal reference:
200626.HCF2WBGXF.ND23
KRKD_GFPi_10h_DU_exp3_b8


title: control knockdown (GFP) in d10 gamergate - rep 9

description:
gamergate.GFPi.rep9
internal reference:
200626.HCF2WBGXF.H005
KRKD_GFPi_10h_DU_exp3_b9


title: control knockdown (GFP) in d10 gamergate - rep 4

description:
gamergate.GFPi.rep4
internal reference:
200508.H5H5HBGXF.H092
KRKD_GFPi_10h_DU_exp2_b4


title: control knockdown (GFP) in d10 gamergate - rep 7

description:
gamergate.GFPi.rep7
internal reference:
200626.HCF2WBGXF.ND14
KRKD_GFPi_10h_DU_exp3_b7


title: control knockdown (GFP) in d10 gamergate - rep 6

description:
gamergate.GFPi.rep6
internal reference:
200626.HCF2WBGXF.ND92
KRKD_GFPi_10h_DU_exp3_b6


title: control knockdown (GFP) in d10 gamergate - rep 2

description:
gamergate.GFPi.rep2
internal reference:
200508.H5H5HBGXF.b0412
KRKD_GFPi_10h_DU_exp2_b2


title: control knockdown (GFP) in d10 gamergate - rep 5

description:
gamergate.GFPi.rep5
internal reference:
200626.HCF2WBGXF.ND83
KRKD_GFPi_10h_DU_exp3_b5


title: control knockdown (GFP) in d10 gamergate - rep 3

description:
gamergate.GFPi.rep3
internal reference:
200508.H5H5HBGXF.H066
KRKD_GFPi_10h_DU_exp2_b3


title: control knockdown (GFP) in d10 worker - rep 3

description:
worker.GFPi.rep3
internal reference:
200626.HCF2WBGXF.b0808
KRKD_GFPi_10h_CW_exp2_b3


title: control knockdown (GFP) in d10 worker - rep 8

description:
worker.GFPi.rep8
internal reference:
200626.HCF2WBGXF.ND64
KRKD_GFPi_10h_CW_exp3_b8


title: control knockdown (GFP) in d10 worker - rep 7

description:
worker.GFPi.rep7
internal reference:
200626.HCF2WBGXF.ND32
KRKD_GFPi_10h_CW_exp3_b7


title: 20E -> JH3 - 24 h - rep 2

description:
neu.20E.to.JH3.24h.rep2
internal reference:
191211.HHFVFBGXC.b0901
JH3_24h_bg_20E_s84

source_name: primary neuronal cultures

growth_protocol: Single-cell suspensions from central brains were plated on poly-D-lysin-coated plates in complete growing media (4 : 6, neurobasal : DMEM medium with 10 mM HEPES, 1x non-essential amino acids, 1x B27 supplement, 1x insulin-transferrin-selenium, 240 nM progesterone and 5 % (v/v) honeybee pupal extract). Cultures were further supplemented with either 2 µM 20E or 2 µM JH3. After four days this medium was replaced with one lacking the honeybee pupal extract.

extract_protocol:
Cells were lysed in TRIzol (Thermo Fisher Scientific, MA). RNA was purified and its quality visualized on agarose-formaldehyde gels. Typical yields amounted to 0.6 µg total RNA per central brain.
For library preparation, polyA+ RNA was isolated from 600 ng total RNA using Dynabeads Oligo(dT)25 (Thermo Fisher) and constructed into strand-specific libraries using the dUTP method (Parkhomchuk et al., 2009). UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics, MA), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual- indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter, CA) and quantified by qPCR after amplification.

treatment_protocol: After 5 days in JH3 or 20E, the medium was replaced with one containing 2 µM of the opposite hormone (JH3 for 20E cultures or 20E for JH3 cultures) for different lenghts of time or DMSO for 30 minutes as a control.

value: primary neuronal cultures

tag: culture medium

tag: timepoint


title: 20E -> JH3 - 6 h - rep 3

description:
neu.20E.to.JH3.6h.rep3
internal reference:
191211.HHFVFBGXC.b0308
JH3_6h_bg_20E_s78


title: 20E -> JH3 - 6 h - rep 5

description:
neu.20E.to.JH3.6h.rep5
internal reference:
191211.HHFVFBGXC.b0106
JH3_6h_bg_20E_s80


title: control knockdown (GFP) in d10 worker - rep 2

description:
worker.GFPi.rep2
internal reference:
200626.HCF2WBGXF.b0707
KRKD_GFPi_10h_CW_exp2_b2


title: JH3 -> 20E - 6 h - rep 5

description:
neu.JH3.to.20E.6h.rep5
internal reference:
191211.HHFVFBGXC.ND46
20E_6h_bg_JH3_s53


title: control knockdown (GFP) in d10 worker - rep 6

description:
worker.GFPi.rep6
internal reference:
200626.HCF2WBGXF.ND05
KRKD_GFPi_10h_CW_exp3_b6


title: 20E -> JH3 - 24 h - rep 1

description:
neu.20E.to.JH3.24h.rep1
internal reference:
191211.HHFVFBGXC.H004
JH3_24h_bg_20E_s83


title: 20E -> JH3 - 24 h - rep 3

description:
neu.20E.to.JH3.24h.rep3
internal reference:
191211.HHFVFBGXC.H015
JH3_24h_bg_20E_s85


title: 20E baseline - rep 4

description:
neu.20E.rep4
internal reference:
191211.HHFVFBGXC.ND89
DMSO_30m_bg_20E_s67

value: DMSO


title: control knockdown (GFP) in d10 worker - rep 5

description:
worker.GFPi.rep5
internal reference:
200626.HCF2WBGXF.b1212
KRKD_GFPi_10h_CW_exp2_b5


title: JH3 -> 20E - 6 h - rep 3

description:
neu.JH3.to.20E.6h.rep3
internal reference:
191211.HHFVFBGXC.ND37
20E_6h_bg_JH3_s51


title: JH3 -> 20E - 24 h - rep 4

description:
neu.JH3.to.20E.24h.rep4
internal reference:
191211.HHFVFBGXC.H022
20E_24h_bg_JH3_s61


title: JH3 -> 20E - 30 min - rep 3

description:
neu.JH3.to.20E.30min.rep3
internal reference:
191211.HHFVFBGXC.ND19
20E_30m_bg_JH3_s47


title: JH3 injection - rep7

description:
internal reference:
200212.HWHLLBGXC.b0202
JH3_10h_d10_Inj7_s15

treatment_protocol: Each ant was injected with a calibrated glass capillary needle directly into the head, right below the antennas with 100 ng of 20E or 100 ng of JH3 dissolved in 5 % glucose. 10 hours after the injections, the central brain was dissected in neurobasal medium, and processed for RNA extraction.


title: JH3 injection - rep6

description:
internal reference:
200212.HWHLLBGXC.b1102
JH3_10h_d10_Inj6_s11


title: control knockdown (GFP) in d10 worker - rep 4

description:
worker.GFPi.rep4
internal reference:
200626.HCF2WBGXF.b1111
KRKD_GFPi_10h_CW_exp2_b4


title: control knockdown (GFP) in d10 gamergate - rep 1

description:
gamergate.GFPi.rep1
internal reference:
200508.H5H5HBGXF.b0311
KRKD_GFPi_10h_DU_exp2_b1


title: 20E -> JH3 - 30 min - rep 3

description:
neu.20E.to.JH3.30min.rep3
internal reference:
191211.HHFVFBGXC.ND68
JH3_30m_bg_20E_s73


title: JH3 -> 20E - 24 h - rep 2

description:
neu.JH3.to.20E.24h.rep2
internal reference:
191211.HHFVFBGXC.H009
20E_24h_bg_JH3_s59


title: control knockdown (GFP) in d10 worker - rep 1

description:
worker.GFPi.rep1
internal reference:
200626.HCF2WBGXF.b0606
KRKD_GFPi_10h_CW_exp2_b1


title: 20E -> JH3 - 6 h - rep 4

description:
neu.20E.to.JH3.6h.rep4
internal reference:
191211.HHFVFBGXC.ND47
JH3_6h_bg_20E_s79


title: JH3 injection - rep4

description:
internal reference:
200212.HWHLLBGXC.b0310
JH3_10h_d10_Inj4_s3


title: JH3 injection - rep5

description:
internal reference:
200212.HWHLLBGXC.b0706
JH3_10h_d10_Inj5_s7


title: JH3 injection - rep3

description:
internal reference:
190514.HYFMWBGX9.b0707
JH3_10h_d10_Inj3_s7


title: JH3 injection - rep2

description:
internal reference:
190514.HYFMWBGX9.b0404
JH3_10h_d10_Inj2_s4


title: JH3 injection - rep1

description:
internal reference:
190514.HYFMWBGX9.b0303
JH3_10h_d10_Inj1_s3


title: DMSO injection - rep5

description:
internal reference:
200212.HWHLLBGXC.b0805
DMSO_10h_d10_Inj5_s8


title: DMSO injection - rep4

description:
internal reference:
200212.HWHLLBGXC.b0409
DMSO_10h_d10_Inj4_s4


title: DMSO injection - rep3

description:
internal reference:
190514.HYFMWBGX9.b1212
DMSO_10h_d10_Inj3_s12


title: DMSO injection - rep2

description:
internal reference:
190514.HYFMWBGX9.b1010
DMSO_10h_d10_Inj2_s10


title: 20E injection - rep7

description:
internal reference:
200212.HWHLLBGXC.b0101
20E_10h_d10_Inj7_s14


title: 20E injection - rep6

description:
internal reference:
200212.HWHLLBGXC.b1003
20E_10h_d10_Inj6_s10


title: 20E injection - rep4

description:
internal reference:
200212.HWHLLBGXC.b0211
20E_10h_d10_Inj4_s2


title: 20E injection - rep5

description:
internal reference:
200212.HWHLLBGXC.b0607
20E_10h_d10_Inj5_s6


title: 20E injection - rep1

description:
internal reference:
190514.HYFMWBGX9.b0101
20E_10h_d10_Inj1_s1


title: Hunting worker brain - d120 - rep8

description:
internal reference:
190820.HJCL7BGXB.b0606
W_d120_OW_b4_s62

data_processing:
Reads were demultiplexed using bcl2fastq2 (Illumina) with the options “--mask-short-adapter-reads 20 --minimum-trimmed-read-length 20 --no-lane-splitting --barcode-mismatches 0”. Reads were aligned to the H. saltator v8.5 assembly (Shields et al., 2018) using STAR (Dobin et al., 2013). STAR alignments were performed in two passes, with the first using the options “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 7 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.07 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 250000”, and the second using the options “--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 500000 --alignMatesGapMax 500000 --sjdbFileChrStartEnd [SJ_files]” where “[SJ_files]” corresponds to the splice junctions produced from all first pass runs.
Gene-level read counts were produced using featureCounts (Liao et al., 2014) with the options “-O -M --fraction -s 2 –p”.
Genome_build: v8.5
Supplementary_files_format_and_content: matrix of per-sample normalized FPKM values for all protein-coding genes in the Hsalt NCBI annotation (release 102)

extract_protocol:
Brains were harvested by dissection in neurobasal medium, the central brain region was isolated by removing the optic lobes, gnathal ganglion, and ~95% of the antennal lobes dissected in neurobasal medium (Gibco), and the tissue was then processed for RNA- or ChIP-seq (see below).
For library preparation, polyA+ RNA was isolated from 600 ng total RNA using Dynabeads Oligo(dT)25 (Thermo Fisher) and constructed into strand-specific libraries using the dUTP method (Parkhomchuk et al., 2009). UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics, MA), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual- indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter, CA) and quantified by qPCR after amplification.


title: Hunting worker brain - d120 - rep7

description:
internal reference:
190820.HJCL7BGXB.ND46
W_d120_OW_b4_s61


title: 20E injection - rep2

description:
internal reference:
190514.HYFMWBGX9.b0606
20E_10h_d10_Inj2_s6


title: Hunting worker brain - d120 - rep9

description:
internal reference:
190820.HJCL7BGXB.H014
W_d120_OW_b4_s78


title: Hunting worker brain - d120 - rep6

description:
internal reference:
190820.HJCL7BGXB.b0505
W_d120_OW_b4_s60


title: Hunting worker brain - d120 - rep4

description:
internal reference:
190514.HYFMWBGX9.ND55
W_d120_OW_b1_s63


title: Hunting worker brain - d120 - rep2

description:
internal reference:
190514.HYFMWBGX9.ND10
W_d120_OW_b1_s53


title: Hunting worker brain - d120 - rep5

description:
internal reference:
190820.HJCL7BGXB.b0303
W_d120_OW_b4_s56


title: Hunting worker brain - d120 - rep3

description:
internal reference:
190514.HYFMWBGX9.ND37
W_d120_OW_b1_s59


title: Dueling gamergate brain - d10 - rep4

description:
internal reference:
190218.HGYTJBGX9.b0909
GG_d10_DU_b2_s20


title: Gamergate brain - d20 - rep1

description:
internal reference:
191029.HFLFFBGXC.ND46
GG_d20_G_b5_s30


title: Hunting worker brain - d120 - rep1

description:
internal reference:
190514.HYFMWBGX9.ND01
W_d120_OW_b1_s51


title: JH3 -> 20E - 30 min - rep 1

description:
neu.JH3.to.20E.30min.rep1
internal reference:
191211.HHFVFBGXC.ND10
20E_30m_bg_JH3_s45


title: Dueling gamergate brain - d10 - rep2

description:
internal reference:
190218.HGYTJBGX9.b0707
GG_d10_DU_b2_s18


title: DMSO injection - rep1

description:
internal reference:
190514.HYFMWBGX9.b0909
DMSO_10h_d10_Inj1_s9


title: Dueling gamergate brain - d10 - rep3

description:
internal reference:
190218.HGYTJBGX9.b0808
GG_d10_DU_b2_s19


title: Dueling gamergate brain - d10 - rep1

description:
internal reference:
190218.HGYTJBGX9.b0606
GG_d10_DU_b2_s17


title: Dueling gamergate brain - d10 - rep5

description:
internal reference:
190218.HGYTJBGX9.b1010
GG_d10_DU_b2_s21


title: Dominant gamergate brain - d120 - rep6

description:
internal reference:
190820.HJCL7BGXB.b0808
GG_d120_DG_b4_s66


title: 20E injection - rep3

description:
internal reference:
190514.HYFMWBGX9.b0808
20E_10h_d10_Inj3_s8


title: Dominant gamergate brain - d120 - rep4

description:
internal reference:
190820.HJCL7BGXB.H053
GG_d120_DG_b4_s84


title: Dominant gamergate brain - d120 - rep5

description:
internal reference:
190820.HJCL7BGXB.b0101
GG_d120_DG_b4_s52


title: Dominant gamergate brain - d120 - rep3

description:
internal reference:
190820.HJCL7BGXB.b1212
GG_d120_DG_b4_s74


title: Worker brain - d10 - rep2

description:
internal reference:
190218.HGYTJBGX9.b1111
W_d10_CW_b2_s13


title: Dominant gamergate brain - d120 - rep2

description:
internal reference:
190820.HJCL7BGXB.b1111
GG_d120_DG_b4_s72


title: Worker brain - d10 - rep1

description:
internal reference:
190218.HGYTJBGX9.b0101
W_d10_CW_b2_s12


title: Worker brain - d10 - rep4

description:
internal reference:
190218.HGYTJBGX9.b0505
W_d10_CW_b2_s16


title: Dominant gamergate brain - d120 - rep1

description:
internal reference:
190514.HYFMWBGX9.ND23
GG_d120_DG_b1_s79


title: Worker brain - d10 - rep3

description:
internal reference:
190218.HGYTJBGX9.b0303
W_d10_CW_b2_s14


title: 20E -> JH3 - 30 min - rep 2

description:
neu.20E.to.JH3.30min.rep2
internal reference:
191208.HFK3NBGXC.b1210
JH3_30m_bg_20E_s72


title: 20E -> JH3 - 30 min - rep 1

description:
neu.20E.to.JH3.30min.rep1
internal reference:
190630.HJCKNBGXB.b0905
JH3_30m_bg_20E_s26


title: JH3 baseline - rep 3

description:
neu.JH3.rep3
internal reference:
190630.HJCKNBGXB.ND37
DMSO_30m_bg_JH3_s5


title: JH3 baseline - rep 1

description:
neu.JH3.rep1
internal reference:
191208.HFK3NBGXC.b0112
DMSO_30m_bg_JH3_s42


title: 20E baseline - rep 3

description:
neu.20E.rep3
internal reference:
191208.HFK3NBGXC.b1112
DMSO_30m_bg_20E_s66


title: 20E baseline - rep 5

description:
neu.20E.rep5
internal reference:
191208.HFK3NBGXC.b0711
DMSO_30m_bg_20E_s68


title: 20E baseline - rep 1

description:
neu.20E.rep1
internal reference:
190630.HJCKNBGXB.b0703
DMSO_30m_bg_20E_s24


title: 20E baseline - rep 2

description:
neu.20E.rep2
internal reference:
190630.HJCKNBGXB.b1006
DMSO_30m_bg_20E_s27


title: JH3 -> 20E - 30 min - rep 4

description:
neu.JH3.to.20E.30min.rep4
internal reference:
190630.HJCKNBGXB.ND46
20E_30m_bg_JH3_s6


title: JH3 -> 20E - 6 h - rep 1

description:
neu.JH3.to.20E.6h.rep1
internal reference:
190630.HJCKNBGXB.H035
20E_6h_bg_JH3_s14


title: JH3 -> 20E - 6 h - rep 2

description:
neu.JH3.to.20E.6h.rep2
internal reference:
190630.HJCKNBGXB.b0501
20E_6h_bg_JH3_s16


title: JH3 -> 20E - 6 h - rep 6

description:
neu.JH3.to.20E.6h.rep6
internal reference:
191208.HFK3NBGXC.b0706
20E_6h_bg_JH3_s54


title: JH3 -> 20E - 6 h - rep 4

description:
neu.JH3.to.20E.6h.rep4
internal reference:
191208.HFK3NBGXC.b0607
20E_6h_bg_JH3_s52


title: Late pupa brain - rep4

description:
internal reference:
190630.HJCKNBGXB.ND28
PU_pupa_pupa_b3_s4

value: pupa


title: JH3 -> 20E - 24 h - rep 3

description:
neu.JH3.to.20E.24h.rep3
internal reference:
191208.HFK3NBGXC.b1003
20E_24h_bg_JH3_s60


title: 20E -> JH3 - 6 h - rep 1

description:
neu.20E.to.JH3.6h.rep1
internal reference:
190630.HJCKNBGXB.H338
JH3_6h_bg_20E_s33


title: JH3 -> 20E - 30 min - rep 2

description:
neu.JH3.to.20E.30min.rep2
internal reference:
191208.HFK3NBGXC.b0310
20E_30m_bg_JH3_s46


title: JH3 -> 20E - 24 h - rep 1

description:
neu.JH3.to.20E.24h.rep1
internal reference:
191208.HFK3NBGXC.b0904
20E_24h_bg_JH3_s58


title: Gamergate brain - d20 - rep2

description:
internal reference:
191029.HFLFFBGXC.ND55
GG_d20_G_b5_s31


title: 20E -> JH3 - 6 h - rep 2

description:
neu.20E.to.JH3.6h.rep2
internal reference:
190630.HJCKNBGXB.H356
JH3_6h_bg_20E_s35


title: Late pupa brain - rep1

description:
internal reference:
190630.HJCKNBGXB.ND01
PU_pupa_pupa_b3_s1


title: Gamergate brain - d20 - rep4

description:
internal reference:
191029.HFLFFBGXC.H009
GG_d20_G_b5_s33


title: Late pupa brain - rep3

description:
internal reference:
190630.HJCKNBGXB.ND19
PU_pupa_pupa_b3_s3


title: Worker brain - d20 - rep4

description:
internal reference:
191029.HFLFFBGXC.ND28
W_d20_CW_b5_s28


title: JH3 baseline - rep 2

description:
neu.JH3.rep2
internal reference:
191208.HFK3NBGXC.b0211
DMSO_30m_bg_JH3_s44


title: Gamergate brain - d20 - rep5

description:
internal reference:
191029.HFLFFBGXC.H022
GG_d20_G_b5_s34


title: JH3 baseline - rep 4

description:
neu.JH3.rep4
internal reference:
190630.HJCKNBGXB.ND64
DMSO_30m_bg_JH3_s8


title: Worker brain - d20 - rep3

description:
internal reference:
191029.HFLFFBGXC.ND19
W_d20_CW_b5_s27


title: Gamergate brain - d20 - rep3

description:
internal reference:
191029.HFLFFBGXC.ND64
GG_d20_G_b5_s32


title: Late pupa brain - rep2

description:
internal reference:
190630.HJCKNBGXB.ND10
PU_pupa_pupa_b3_s2


title: JH3 -> 20E - 30 min - rep 5

description:
neu.JH3.to.20E.30min.rep5
internal reference:
190630.HJCKNBGXB.H009
20E_30m_bg_JH3_s9


title: Worker brain - d20 - rep1

description:
internal reference:
191029.HFLFFBGXC.b1010
W_d20_CW_b5_s22


title: Worker brain - d20 - rep2

description:
internal reference:
191029.HFLFFBGXC.b1111
W_d20_CW_b5_s23


title: uterus_Female_104_rep4

status: Public on Nov 01 2021

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

data_processing:
The adapter sequences were removed with fastp 0.23.2 software (http://opengene.org/fastp/fastp.0.23.2), followed by a quality filter and a length filter. Reads with more than 2 “N” bases were discarded. The clipped reads with length between 16 and 35 nt were retained for alignment to various transcript types, including miRNA (miRbase v22.1, http://www.mirbase.org/), piRNA (piRBase, http://www.regulatoryrna.org/database/piRNA/download.html), tRNA (GtRNAdb, http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Rnorv7/Rnorv7-seq.html), other RNA (NCBI transcriptome, https://www.ncbi.nlm.nih.gov/genome/73), and the rat genome (Rn7, https://hgdownload.soe.ucsc.edu/downloads.html#mammals). The alignment was performed with Bowtie 1.3.1 (http://bowtie-bio.sourceforge.net/manual.shtml) with less than 2 mismatched bases allowed.
miRDeep2.0.1.3 was used for novel miRNA predicting and mapping.
Genome_build: rat genome rn7 download from UCSC and miRBase v22.1.
Sequence of novel miRNAs are available in file on series record.
Supplementary_files_format_and_content: read count

organism: Rattus norvegicus

source_name: Uterus

growth_protocol: pair-housed under standard conditions

extract_protocol:
Total RNA was extracted from ~30 mg of ground tissue by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including treatment with DNase.
Small RNA libraries were constructed using Illumina TruSeq Small RNA Library Prep kit.

treatment_protocol: Each whole organ was individually ground into a fine powder

value: Fisher 344

value: Uterus

tag: age (weeks)

tag: Sex

value: Female

tag: replicate


title: uterus_Female_006_rep3


title: uterus_Female_021_rep4


title: uterus_Female_021_rep2


title: uterus_Female_021_rep1


title: uterus_Female_104_rep3


title: uterus_Female_021_rep3


title: uterus_Female_104_rep2


title: uterus_Female_104_rep1


title: uterus_Female_006_rep4


title: uterus_Female_002_rep4


title: uterus_Female_002_rep2


title: uterus_Female_002_rep3


title: uterus_Female_006_rep2


title: uterus_Female_002_rep1


title: testis_Male_104_rep4

source_name: Testes

value: Testes

value: Male


title: testis_Male_021_rep1


title: testis_Male_021_rep3


title: testis_Male_006_rep4


title: testis_Male_104_rep2


title: testis_Male_006_rep3


title: testis_Male_006_rep2


title: testis_Male_021_rep2


title: testis_Male_021_rep4


title: testis_Male_002_rep3


title: testis_Male_104_rep1


title: testis_Male_006_rep1


title: thymus_Male_104_rep4

source_name: Thymus

value: Thymus


title: thymus_Male_021_rep3


title: thymus_Male_021_rep1


title: thymus_Male_104_rep3


title: thymus_Male_021_rep2


title: thymus_Male_104_rep2


title: testis_Male_002_rep2


title: thymus_Male_006_rep4


title: thymus_Male_021_rep4


title: thymus_Male_104_rep1


title: thymus_Male_006_rep3


title: thymus_Male_002_rep4


title: thymus_Male_002_rep3


title: thymus_Male_006_rep2


title: thymus_Male_006_rep1


title: testis_Male_002_rep1


title: uterus_Female_006_rep1


title: testis_Male_104_rep3


title: thymus_Male_002_rep1


title: thymus_Male_002_rep2


title: thymus_Female_104_rep4


title: thymus_Female_021_rep3


title: thymus_Female_104_rep1


title: thymus_Female_104_rep2


title: thymus_Female_006_rep4


title: thymus_Female_021_rep1


title: thymus_Female_021_rep2


title: thymus_Female_002_rep2


title: thymus_Female_006_rep3


title: spleen_Male_021_rep4

source_name: Spleen

value: Spleen


title: thymus_Female_006_rep1


title: testis_Male_002_rep4


title: spleen_Male_104_rep4


title: spleen_Male_104_rep1


title: thymus_Female_002_rep1


title: spleen_Male_021_rep2


title: spleen_Male_021_rep3


title: spleen_Male_104_rep3


title: thymus_Female_002_rep4


title: spleen_Male_006_rep2


title: spleen_Male_006_rep3


title: thymus_Female_006_rep2


title: thymus_Female_021_rep4


title: spleen_Male_104_rep2


title: spleen_Male_006_rep1


title: spleen_Male_002_rep3


title: spleen_Male_002_rep4


title: spleen_Male_002_rep1


title: spleen_Female_104_rep1


title: spleen_Male_002_rep2


title: spleen_Female_104_rep2


title: thymus_Female_104_rep3


title: spleen_Female_104_rep4


title: spleen_Female_104_rep3


title: spleen_Male_006_rep4


title: spleen_Male_021_rep1


title: thymus_Female_002_rep3


title: spleen_Female_021_rep4


title: spleen_Female_021_rep3


title: spleen_Female_021_rep1


title: spleen_Female_006_rep4


title: spleen_Female_002_rep4


title: spleen_Female_006_rep1


title: spleen_Female_002_rep3


title: spleen_Female_002_rep1


title: spleen_Female_006_rep3


title: skeletal muscle_Male_104_rep2

source_name: Muscle

value: Muscle


title: skeletal muscle_Male_021_rep4


title: skeletal muscle_Male_104_rep3


title: skeletal muscle_Male_104_rep4


title: skeletal muscle_Male_104_rep1


title: spleen_Female_006_rep2


title: skeletal muscle_Male_021_rep1


title: skeletal muscle_Male_021_rep2


title: skeletal muscle_Male_021_rep3


title: skeletal muscle_Male_006_rep4


title: spleen_Female_021_rep2


title: skeletal muscle_Male_006_rep3


title: skeletal muscle_Male_002_rep4


title: skeletal muscle_Male_002_rep1


title: skeletal muscle_Male_002_rep3


title: skeletal muscle_Female_104_rep2


title: skeletal muscle_Female_104_rep3


title: skeletal muscle_Female_104_rep4


title: skeletal muscle_Female_021_rep4


title: spleen_Female_002_rep2


title: skeletal muscle_Female_021_rep1


title: skeletal muscle_Female_104_rep1


title: skeletal muscle_Female_006_rep1


title: skeletal muscle_Female_021_rep2


title: skeletal muscle_Female_006_rep3


title: skeletal muscle_Female_002_rep4


title: skeletal muscle_Male_006_rep2


title: skeletal muscle_Female_002_rep3


title: skeletal muscle_Female_006_rep2


title: skeletal muscle_Female_006_rep4


title: skeletal muscle_Female_002_rep2


title: skeletal muscle_Female_002_rep1


title: liver_Male_104_rep4

source_name: Liver

value: Liver


title: liver_Male_104_rep2


title: skeletal muscle_Male_006_rep1


title: liver_Male_021_rep4


title: liver_Male_104_rep1


title: liver_Male_104_rep3


title: liver_Male_021_rep3


title: liver_Male_021_rep1


title: liver_Male_006_rep4


title: skeletal muscle_Male_002_rep2


title: liver_Male_006_rep1


title: liver_Male_002_rep4


title: liver_Male_002_rep3


title: liver_Male_002_rep2


title: liver_Female_104_rep4


title: liver_Male_002_rep1


title: liver_Female_104_rep2


title: liver_Female_104_rep1


title: liver_Female_021_rep4


title: liver_Female_021_rep2


title: liver_Female_021_rep1


title: liver_Male_021_rep2


title: liver_Female_021_rep3


title: liver_Female_006_rep1


title: liver_Female_002_rep3


title: liver_Female_006_rep2


title: liver_Male_006_rep3


title: liver_Female_006_rep3


title: liver_Female_002_rep4


title: liver_Female_006_rep4


title: liver_Female_002_rep1


title: liver_Female_002_rep2


title: lung_Male_104_rep4

source_name: Lung

value: Lung


title: lung_Male_104_rep3


title: lung_Male_104_rep2


title: liver_Male_006_rep2


title: lung_Male_104_rep1


title: lung_Male_021_rep4


title: lung_Male_021_rep3


title: liver_Female_104_rep3


title: lung_Male_021_rep1


title: lung_Male_006_rep3


title: lung_Male_006_rep2


title: lung_Male_021_rep2


title: lung_Male_002_rep3


title: lung_Male_002_rep4


title: lung_Male_006_rep1


title: lung_Female_104_rep4


title: lung_Male_002_rep2


title: lung_Male_006_rep4


title: lung_Male_002_rep1


title: lung_Female_104_rep2


title: lung_Female_104_rep1


title: lung_Female_006_rep4


title: lung_Female_021_rep4


title: lung_Female_021_rep3


title: lung_Female_104_rep3


title: lung_Female_006_rep3


title: lung_Female_002_rep4


title: lung_Female_021_rep2


title: lung_Female_002_rep3


title: skeletal muscle_Female_021_rep3


title: lung_Female_002_rep1


title: kidney_Male_104_rep3

source_name: Kidney

value: Kidney


title: kidney_Male_104_rep1


title: lung_Female_002_rep2


title: lung_Female_021_rep1


title: kidney_Male_104_rep4


title: lung_Female_006_rep1


title: kidney_Male_006_rep2


title: kidney_Male_021_rep2


title: kidney_Male_104_rep2


title: kidney_Male_021_rep3


title: kidney_Male_002_rep4


title: kidney_Female_104_rep2


title: kidney_Female_104_rep4


title: kidney_Male_021_rep1


title: kidney_Female_104_rep1


title: kidney_Male_002_rep3


title: kidney_Male_006_rep1


title: lung_Female_006_rep2


title: kidney_Male_002_rep1


title: kidney_Male_021_rep4


title: kidney_Female_021_rep4


title: kidney_Female_021_rep3


title: kidney_Female_021_rep2


title: kidney_Female_006_rep4


title: kidney_Male_002_rep2


title: kidney_Male_006_rep3


title: kidney_Female_104_rep3


title: kidney_Male_006_rep4


title: kidney_Female_021_rep1


title: kidney_Female_002_rep4


title: kidney_Female_002_rep1


title: kidney_Female_006_rep3


title: kidney_Female_006_rep2


title: heart_Male_104_rep4

source_name: Heart

value: Heart


title: kidney_Female_002_rep3


title: kidney_Female_002_rep2


title: heart_Male_104_rep3


title: heart_Male_104_rep2


title: heart_Male_021_rep4


title: heart_Male_006_rep2


title: heart_Male_006_rep3


title: heart_Male_021_rep3


title: heart_Male_002_rep2


title: heart_Male_006_rep1


title: heart_Male_021_rep2


title: heart_Male_006_rep4


title: heart_Male_002_rep1


title: heart_Male_002_rep4


title: heart_Female_104_rep3


title: heart_Female_104_rep4


title: heart_Female_021_rep4


title: kidney_Female_006_rep1


title: heart_Female_104_rep2


title: heart_Female_021_rep3


title: heart_Female_002_rep4


title: heart_Female_021_rep1


title: heart_Female_021_rep2


title: heart_Female_006_rep2


title: heart_Female_002_rep3


title: heart_Male_104_rep1


title: heart_Female_006_rep3


title: heart_Female_006_rep4


title: heart_Male_021_rep1


title: heart_Male_002_rep3


title: heart_Female_006_rep1


title: brain_Male_104_rep1

source_name: Brain

value: Brain


title: heart_Female_002_rep2


title: heart_Female_002_rep1


title: brain_Male_021_rep2


title: brain_Male_021_rep3


title: brain_Male_104_rep4


title: brain_Male_104_rep2


title: brain_Male_104_rep3


title: heart_Female_104_rep1


title: brain_Male_021_rep4


title: brain_Male_021_rep1


title: brain_Male_006_rep2


title: brain_Male_006_rep4


title: brain_Male_006_rep1


title: brain_Male_006_rep3


title: brain_Male_002_rep4


title: brain_Male_002_rep3


title: brain_Female_104_rep3


title: brain_Female_104_rep1


title: brain_Female_021_rep4


title: brain_Female_104_rep2


title: brain_Female_021_rep2


title: brain_Female_006_rep2


title: brain_Female_006_rep4


title: brain_Female_002_rep3


title: brain_Female_021_rep3


title: brain_Female_104_rep4


title: brain_Female_002_rep4


title: brain_Female_006_rep3


title: brain_Female_006_rep1


title: brain_Female_002_rep1


title: adrenal gland_Male_104_rep1

source_name: Adrenal

value: Adrenal


title: adrenal gland_Male_104_rep4


title: adrenal gland_Male_104_rep2


title: adrenal gland_Male_021_rep3


title: brain_Female_021_rep1


title: adrenal gland_Male_021_rep1


title: brain_Male_002_rep2


title: adrenal gland_Male_006_rep4


title: brain_Male_002_rep1


title: adrenal gland_Male_006_rep3


title: adrenal gland_Male_006_rep1


title: adrenal gland_Male_006_rep2


title: adrenal gland_Male_002_rep4


title: adrenal gland_Male_002_rep3


title: adrenal gland_Male_002_rep2


title: adrenal gland_Male_002_rep1


title: adrenal gland_Female_104_rep4


title: brain_Female_002_rep2


title: adrenal gland_Male_104_rep3


title: adrenal gland_Female_104_rep2


title: adrenal gland_Female_104_rep3


title: adrenal gland_Female_021_rep4


title: adrenal gland_Female_104_rep1


title: adrenal gland_Female_021_rep3


title: adrenal gland_Male_021_rep2


title: adrenal gland_Female_021_rep1


title: adrenal gland_Female_006_rep4


title: adrenal gland_Male_021_rep4


title: adrenal gland_Female_006_rep1


title: adrenal gland_Female_006_rep3


title: adrenal gland_Female_021_rep2


title: adrenal gland_Female_006_rep2


title: adrenal gland_Female_002_rep3


title: adrenal gland_Female_002_rep1


title: adrenal gland_Female_002_rep4


title: GW9T

status: Public on Oct 27 2021

city: Beijing

first: Xianming

last: Wu

state: Chaoyang District

address: Unit 2, No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Base call files were demultiplexed into FASTQ files by Cellranger 3.1.0
FASTQ files were analysized by "cellranger count" function of Cellranger 3.1.0
"filtered_feature_bc_matrix" was produced and stored in the Market Exchange Format (MEX) for sparse matrices
Genome_build: GRCh38
Supplementary_files_format_and_content: MEX format for sparse matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Cells From Spinal Cord

extract_protocol:
Fetal spinal cords were collected in ice-cold preserve medium containing. The spinal cord was dissected and placed in Hanks Balanced Solution without calcium and magnesium (HBSS, Life Technologies 14185045). The tissue was digested according to the protocol of papain dissociation kit (Worthington Biochemical). In brief spinal cord roughly dissected into small pieces, tissue was then digested in Papain digest medium for 40min at 37°C to dissociate the cells. The cell suspension was pipetted further and filtered twice through 0.35um filters. Centrifuged at 300g 4℃ for 5 min to obtain a cell pellet. After the digestion medium was carefully removed, cell pellet was resuspended in 500 μ HBSS medium and kept on ice. The nuclear islation performed according to the protocol of Nuclei Isolation Kit: Nuclei EZ Prep (NUC101-1KT)
RNA libraries were prepared for sequencing using standard Illumina protocols, the single cells suspension was loaded onto the Chromium single cell controller (10xGenomics). Library preparation was performed using the single cell 3 'Library and Gel Bead Kit V2 (10xGenomics, PN-120235) /V3 (10xGenomics, 1000075) and Chromium Single Cell B Chip Kit (10xGenomics, PN-120236). cDNA amplification involved 11 PCR cycles. Raw sequencing data was processed using Cell Ranger analysis pipeline. Reads were aligned to human genome version GRCh38.
According to the manufacture's introduction, snRNA-seq/scRNA-seq libraries were constructed using Single Cell 3' Library and Gel Bead Kit V3. Finally sequencing was performed on the Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell and 150 bp (PE150) paired-end reads (performed by CapitalBio, Beijing).

value: Spinal Cord

tag: age

value: 9 weeks after gestation

tag: gender

tag: molecule

value: Total RNA

tag: region

value: Thoracic


title: GW9C

tag: tissue

value: Cervical


title: GW8L_01

value: 8 weeks after gestation

value: Female

value: Lumbar


title: GW8S_02

value: Male

value: Whole spinal cord


title: GW8S_02NC

source_name: Nuclear From Spinal Cord

value: Nuclear RNA


title: GW8C_01


title: GW7S_NC

value: 7 weeks after gestation


title: GW7S


title: GW25C

value: 25 weeks after gestation


title: GW24T

value: 24 weeks after gestation


title: GW24L


title: GW24C


title: GW23S

value: 23 weeks after gestation


title: GW23S_NC


title: GW22T

value: 22 weeks after gestation


title: GW22L


title: adrenal gland_Female_002_rep2

tag: strain

value: Fisher 344

value: Adrenal


title: GW20T_02

value: Spinal Cord

value: 20 weeks after gestation


title: GW21L_NC

value: 21 weeks after gestation


title: GW22C

value: Total RNA

value: Cervical


title: GW20L_02

value: Female


title: GW20L_NC

value: Lumbar


title: GW20T_NC

value: Male

value: Thoracic


title: GW21T_NC

value: Nuclear RNA


title: GW20C_NC


title: GW21C_NC


title: GW19C

value: 19 weeks after gestation


title: GW20C_02


title: GW20T_01


title: GW18C_NC

value: 18 weeks after gestation


title: GW25T

value: 25 weeks after gestation


title: GW18L_NC


title: GW18T_NC


title: GW17T_02

value: 17 weeks after gestation


title: GW19T


title: GW17T_01


title: GW17L_02


title: GW17C_02


title: GW17L_01


title: GW17C_01


title: GW16L

value: 16 weeks after gestation


title: GW15T_02

value: 15 weeks after gestation


title: GW16C


title: GW16T


title: GW19L


title: GW15L_02


title: GW15L_01


title: GW15T_01


title: GW14T_NC

value: 14 weeks after gestation


title: GW20C_01

value: Spinal Cord


title: GW13T_01

value: 13 weeks after gestation


title: GW15C_02


title: GW13T_02


title: GW14L_NC


title: GW15C_01


title: GW13L_02


title: GW14C_NC


title: GW13C_02


title: GW12T_01

value: 12 weeks after gestation


title: GW12L_02

value: Total RNA


title: GW12C_02

value: Cervical


title: GW11T_NC

value: 11 weeks after gestation


title: GW13C_01


title: GW12C_01


title: GW11L

value: Lumbar


title: GW11C

value: Male


title: GW10T_02

value: 10 weeks after gestation

value: Female

value: Thoracic


title: GW10L_02NC

value: Nuclear RNA


title: GW10T_01NC


title: GW10T_02NC


title: GW10L_02


title: GW10C_02


title: GW10L_01NC


title: GW12T_02


title: GW10C_02NC


title: ZAP70 GFP +

status: Public on Jul 07 2021

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

description: Isolated from humanized mice

data_processing:
FASTQ were generated using the 10x Genomic’s Cell Ranger pipeline version 3.1.0
Reads were aligned to the GRCh38-alts-ensembl-2.0.0 assembly to generate VDJ counts and identify CDR3 sequences.
Genome_build: Hg38
Supplementary_files_format_and_content: CDR3 contigs generated by CellRanger were combined across all conditions and provided as a dataframe.

source_name: Naïve B-cells

extract_protocol:
Purified B-cells were obtained by FACS sorting and single-cell RNA extracted using 10X platform
Human VDJ sequencing libraries were generated with Chromium Single Cell 5’ Reagent Kits (10x Genomics) according to manufacturer’s protocol.

tag: mouse host strain

tag: markers


title: ZAP70 GFP -

description: Isolated from humanized mice


title: UI_ctrl

status: Public on Sep 07 2021

city: Bethesda

first: Jason

last: Sinclair

state: MD

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

data_processing:
Binary Base Call (BCL) files generated from an Illumina 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 (10x Genomics)
Cell Ranger Version 3.0.2. was used to demultiplex, for barcode processing, for single cell gene counts, and aggregating files.
Further analyses of the samples was performed using Loupe Cell Browser (10x Genomics)
Genome_build: Danio_Rerio_11
Supplementary_files_format_and_content: clouple files are provided which can be visiualized with the Loupe Cell Browser (10x Genomics)

source_name: Regenerating embryonic zebrafish tail

extract_protocol:
Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase.
cDNA libraries was generatated with Chromium Controller and Chromium Single Cell 3' GEM, Library and Gel Bead Kit V3 (10x Genomics)

tag: embryo age

value: 3 days post-fertilization

tag: treatment


title: UI_2DG

source_name: Developing embryonic zebrafish tail

value: 100 mM 2-deoxyglucose


title: EV GFP -

description: Isolated from humanized mice


title: NSCLC.P019.post.01

status: Public on Oct 06 2021

first: Zemin

last: Zhang

address: No. 5, Summer Palace Road, Haidian District, Beijing

department: BIOPIC

institute: Peking University

description: P019.blood.post.Tcell.Seurat.object.rds.gz

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 3.0.2) against the GRCh38 human reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 3.1) with the manufacturer-supplied human VDJ reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cellranger version 3.0.2

extract_protocol:
Fresh tumour biopsies were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 μm SmartStrainer and centrifuged at 400g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS). The concentration of single-cell suspensions was adjusted to 500~1200 cells/ul. 10,000~18,000 cells were used for the 10x Chromium Single cell 5’ and VDJ library construction (10x Genomics), according to the manufacturer’s instructions.
10x Chromium Single cell 5’ + VDJ Library

tag: patient id

tag: disease state

value: non-small-cell lung cancer patients

tag: condition

value: On-treatment

tag: platform

value: 10X Genomics


title: TCL1_ZAP70_KI_rep4

data_processing:
Transcript abundances were estimated with Salmon V1.1.0 against indexes generated with Gencode GRCm38 vM24
Rlog normalised gene level expression values were calculated using tximport v1.16.1 and DESeq2 v1.28.1.
Genome_build: mm10
Supplementary_files_format_and_content: rlog normalised gene expression estimates in csv format

organism: Mus musculus

source_name: Chronic Lymphocytic Leukemia (CLL)

extract_protocol:
Purified B-cells sorted by FACS
Libraries were prepared with Illumina TruSeq2 RNAseq library prep kits according to manufacturers instructions

value: Chronic Lymphocytic Leukemia (CLL)

tag: cell type

value: CLL cells (CD5+CD19+)

value: Spleen


title: EV GFP +

description: Isolated from humanized mice


title: GW11T

value: Spinal Cord

value: Total RNA


title: TCL1_ZAP70_KI_rep1


title: TCL1_ZAP70_WT_rep4


title: GW11L_NC

value: 11 weeks after gestation


title: TCL1_ZAP70_WT_rep3


title: TCL1_ZAP70_WT_rep1


title: GW11C_NC

value: Cervical


title: TCL1_ZAP70_WT_rep2


title: TCL1_ZAP70_KI_rep2


title: GW10C_01NC


title: RB111 (3.5K BAC-CGH)

status: Public on Jul 06 2021

type: genomic

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 51

hyb_protocol: see platform's Manufacture protocol

scan_protocol: ScanArray 4000 (Packard Bioscience)

data_processing:
HG19 version of the genome used, data processed with GLAD algorithm (Hupé et al, Bioinformatics, 2004)
Raw data matrix : raw log ratio values, Processed data matrix: Gap-smoothed log ratio values

source_name: retinoblastoma sample RB111

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A. DNA was then extracted using a standard phenol-chloroform protocol

value: SAMPLE 56

value: retinoblastoma


title: TCL1_ZAP70_KI_rep3


title: RB58 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 47

source_name: retinoblastoma sample RB58

value: SAMPLE 48


title: RB60 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 49

source_name: retinoblastoma sample RB60

value: SAMPLE 50


title: RB61 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 50

source_name: retinoblastoma sample RB61

value: SAMPLE 51


title: RB59 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 48

source_name: retinoblastoma sample RB59

value: SAMPLE 49


title: RB47 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 37

source_name: retinoblastoma sample RB47

value: SAMPLE 38


title: RB57 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 46

source_name: retinoblastoma sample RB57

value: SAMPLE 47


title: RB55 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 44

source_name: retinoblastoma sample RB55

value: SAMPLE 45


title: RB50 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 40

source_name: retinoblastoma sample RB50

value: SAMPLE 41


title: RB56 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 45

source_name: retinoblastoma sample RB56

value: SAMPLE 46


title: RB49 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 39

source_name: retinoblastoma sample RB49

value: SAMPLE 40


title: RB51 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 41

source_name: retinoblastoma sample RB51

value: SAMPLE 42


title: RB42 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 32

source_name: retinoblastoma sample RB42

value: SAMPLE 33


title: RB46 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 36

source_name: retinoblastoma sample RB46

value: SAMPLE 37


title: RB52 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 42

source_name: retinoblastoma sample RB52

value: SAMPLE 43


title: RB48 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 38

source_name: retinoblastoma sample RB48

value: SAMPLE 39


title: RB45 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 35

source_name: retinoblastoma sample RB45

value: SAMPLE 36


title: RB44 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 34

source_name: retinoblastoma sample RB44

value: SAMPLE 35

value: retinoblastoma


title: RB41 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 31

source_name: retinoblastoma sample RB41

value: SAMPLE 32


title: RB39 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 29

source_name: retinoblastoma sample RB39

value: SAMPLE 30


title: RB54 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 43

source_name: retinoblastoma sample RB54

value: SAMPLE 44


title: RB38 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 28

source_name: retinoblastoma sample RB38

value: SAMPLE 29


title: RB34 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 25

source_name: retinoblastoma sample RB34

value: SAMPLE 26


title: RB35 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 26

source_name: retinoblastoma sample RB35

value: SAMPLE 27


title: RB32 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 23

source_name: retinoblastoma sample RB32

value: SAMPLE 24


title: RB31 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 22

source_name: retinoblastoma sample RB31

value: SAMPLE 23


title: RB33 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 24

source_name: retinoblastoma sample RB33

value: SAMPLE 25


title: RB37 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 27

source_name: retinoblastoma sample RB37

value: SAMPLE 28


title: RB43 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 33

source_name: retinoblastoma sample RB43

value: SAMPLE 34


title: RB40 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 30

source_name: retinoblastoma sample RB40

value: SAMPLE 31


title: RB27 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 19

source_name: retinoblastoma sample RB27

value: SAMPLE 19


title: RB28 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 20

source_name: retinoblastoma sample RB28

value: SAMPLE 20


title: RB25 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 18

source_name: retinoblastoma sample RB25

value: SAMPLE 18


title: RB22 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 15

source_name: retinoblastoma sample RB22

value: SAMPLE 15


title: RB30 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 21

source_name: retinoblastoma sample RB30

value: SAMPLE 22

value: retinoblastoma


title: RB12 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 10

source_name: retinoblastoma sample RB12

value: SAMPLE 10


title: RB14 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 12

source_name: retinoblastoma sample RB14

value: SAMPLE 12


title: RB10 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 8

source_name: retinoblastoma sample RB10

value: SAMPLE 8


title: RB15 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 13

source_name: retinoblastoma sample RB15

value: SAMPLE 13


title: RB21 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 14

source_name: retinoblastoma sample RB21

value: SAMPLE 14


title: RB9 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 7

source_name: retinoblastoma sample RB9

value: SAMPLE 7


title: RB4 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 4

source_name: retinoblastoma sample RB4

value: SAMPLE 4


title: RB6 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 5

source_name: retinoblastoma sample RB6

value: SAMPLE 5


title: RB7 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 6

source_name: retinoblastoma sample RB7

value: SAMPLE 6


title: RB3 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 3

source_name: retinoblastoma sample RB3

value: SAMPLE 3


title: RB13 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 11

source_name: retinoblastoma sample RB13

value: SAMPLE 11


title: RB24 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 17

source_name: retinoblastoma sample RB24

value: SAMPLE 17


title: RB11 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 9

source_name: retinoblastoma sample RB11

value: SAMPLE 9


title: RB1 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 1

source_name: retinoblastoma sample RB1

value: SAMPLE 1


title: RB222 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 23

source_name: retinoblastoma sample RB222

value: SAMPLE 79


title: RB2 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 2

source_name: retinoblastoma sample RB2

value: SAMPLE 2


title: RB224 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 25

source_name: retinoblastoma sample RB224

value: SAMPLE 81

value: retinoblastoma


title: RB221 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 22

source_name: retinoblastoma sample RB221

value: SAMPLE 78


title: RB225 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 26

source_name: retinoblastoma sample RB225

value: SAMPLE 82


title: RB23 (3.5K BAC-CGH)

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 16

source_name: retinoblastoma sample RB23

value: SAMPLE 16


title: RB223 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 24

source_name: retinoblastoma sample RB223

value: SAMPLE 80


title: RB220 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 21

source_name: retinoblastoma sample RB220

value: SAMPLE 77


title: RB218 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 19

source_name: retinoblastoma sample RB218

value: SAMPLE 75


title: RB215 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 16

source_name: retinoblastoma sample RB215

value: SAMPLE 72


title: RB214 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 15

source_name: retinoblastoma sample RB214

value: SAMPLE 71


title: RNAseq - AID-JARID2 CPs - auxin - rep2

status: Public on Apr 21 2021

data_processing:
Paired-end RNA-seq reads were aligned the Mus musculus mm10 genome using STAR 2.6.1d (Dobin et al., 2013) with default parameters except –peOverlapNbasesMin set to 10 and –alignIntronMax set to 100000.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-separated file containg TPMs (transcripts per million) for each NCBI annotated gene with a gene symbol.

source_name: CPs

growth_protocol: C57BL/6 mouse ESCs (ATCC) were cultured on gelatinized dishes in serum-free N2B27 media  (1:1 mix of neurobasal medium (Gibco) and DMEM/F12 (Gibco), 100 mM MEM nonessential amino acids (Sigma), 55 µM 2-mercaptoethanol (Gibco), 2 mM L-glutamine (Sigma), 0.5% penicillin/streptomycin (Sigma), 1x N27 and 1x B27 (Gibco)) supplemented with 100 U/mL leukemia inhibitory factor (LIF) (Chemicon), 3 µM CHIR99021 (Millipore) and 1 µM PD0325901 (Millipore). Cells were passaged every 2–3 days via dissociation in 0.05% trypsin (Genesee Scientific). Differentiation was performed as follows: ESCs were seeded on bacterial petri dishes at 75,000 cells/mL and aggregated into embryoid bodies (EBs) for 48h in serum-free differentiation media (3:1 IMDM to Ham’s F-12, 0.05% BSA, 2mM L-glutamine, 1x N2, 1x B27 (minus vitamin A) supplemented with 50 µg/mL L-ascorbic acid and 4.5 x 10-4 M MTG. EBs were then dissociated and seeded at 75,000 cells/mL in bacterial petri dishes to reaggregate for 43 hr in the presence of 5 ng/mL human VEGF, and human Activin A and human BMP4. EBs were dissociated and plated at 300,000 cells/cm2 for monolayer culture in StemPro-34 supplemented with 5 ng/mL human VEGF, 10 ng/mL human basic FGF and 25 ng/mL FGF10. Cells reached the cardiac precursor stage 32 h after plating in StemPro-34 and were harvested for RNA analysis.

extract_protocol:
Cells were rinsed once with PBS and lysed via direct addition of TRIzol reagent (Thermo Fisher Scientific). Total cellular RNA was purified using the Direct-zol RNA Miniprep kit (Zymo Research).
PolyA+ RNA was isolated from 500 ng total RNA using Dynabeads Oligo(dT)25 beads (Thermo Fisher) and constructed into strand-specific libraries using the dUTP method. UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter) and quantified by qPCR before and after amplification.
Stranded mRNA-seq

treatment_protocol: To induce degradation of AID-tagged proteins (SUZ12, MTF2. or JARID2), indole-3-acetic acid (IAA, chemical analog of auxin) was added to the cell culture medium at a final concentration of 50 µM from a 500 mM stock dissolved in sterile water that was stored long-term at -20ºC.

tag: technology

value: RNA-seq

tag: genotype

value: AID-JARID2, Tir1

value: auxin


title: HEK293T-RBFOX2-STAMP none rep1

status: Public on May 09 2021

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Raw reads were trimmed using cutadapt (v1.14) using the following parameters -O 5 -f  fastq --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -o data.fastqTr.fq -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT data.fastq.gz
Trimmed reads were mapped to and filtered of repeat elements (RepBase 18.05) with STAR (2.4.0i) using the following parameters: --alignEndsType  EndToEnd  --genomeDir  repbase  --genomeLoad  NoSharedMemory  --outBAMcompression  10  --outFileNamePrefix  data  --outFilterMultimapNmax  10  --outFilterMultimapScoreRange  1  --outFilterScoreMin  10  --outFilterType  BySJout  --outReadsUnmapped  Fastx  --outSAMattrRGline  ID:foo  --outSAMattributes  All  --outSAMmode  Full  --outSAMtype  BAM  Unsorted  --outSAMunmapped  Within  --outStd  Log  --readFilesIn data.fastqTr.fq  --runMode  alignReads  --runThreadN  8
Reads unmapped to repeat elements were mapped to the human genome with STAR using the same parameters as the previous step, using an hg19 index in place of the repeat element index
Subread featureCounts (-a gencode.v19.annotation.gtf -s 2 -o counts.txt data.bam) was used to count features using human annotations (Gencode v19)
Edits were called using SAILOR (http://github.com/yeolab/sailor) using default parameters and dbSNP (v147) to remove known SNPs.
bigwig files were generated from filtered BAM files (intermediates from SAILOR), using the following commands from BedTools (v2.27.1). :     bedtools genomecov -split -strand - -g hg19.chrom.sizes -bg -ibam fwd.bam > fwd.bg  bedtools sort -I fwd.bg > fwd.sorted.bg   bedGraphToBigWig fwd.sorted.bg hg19.chrom.sizes fwd.sorted.bw    bedtools genomecov -split -strand + -g hg19.chrom.sizes -bg -ibam rev.bam > rev.bg  bedtools sort -I rev.bg > rev.sorted.bg   bedGraphToBigWig rev.sorted.bg hg19.chrom.sizes rev.sorted.bw
Genome_build: hg19

growth_protocol: All stable STAMP HEK293T cell lines were generated using human lenti-X HEK293T cells (HEK293XT, Takara Bio) which are derived from transformed female human embryonic kidney tissue. Cells were maintained in DMEM (4.5 g/L D-glucose) supplemented with 10% FBS (Gibco) at 37o C with 5% CO2. Cells were periodically passaged once at 70-90% confluency by dissociating with TrypLE Express Enzyme (Gibco) at a ratio of 1:10.

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
Illumina TruSeq stranded mRNA or total RNA

treatment_protocol: For STAMP fusion protein expression STAMP stable HEK293T cells were induced with 50ng/ml (low) or 1ug/ml (high) doxycycline in DMEM for 24-72 hours, followed by Trizol extraction and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol.  Uninduced cells of the same genetic background were used as negative controls. For mTOR perturbation experiments, cells were treated with 100nM Torin-1 or 100nM insulin alongside 1ug/ml doxycycline induction and harvested for RNA after 72 hours 37C incubation.

tag: cell line


title: RB211 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 12

source_name: retinoblastoma sample RB211

value: SAMPLE 68


title: RB212 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 13

source_name: retinoblastoma sample RB212

value: SAMPLE 69


title: RB213 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 14

source_name: retinoblastoma sample RB213

value: SAMPLE 70


title: RNAseq - MTF2-AID CPs - auxin - rep1

value: MTF2-AID, Tir1


title: RNAseq - MTF2-AID CPs - auxin - rep2


title: RNAseq - AID-JARID2 CPs - auxin - rep1


title: RNAseq - SUZ12-AID CPs - auxin - rep2

value: SUZ12-AID, Tir1


title: RNAseq - AID-JARID2 CPs - untreated - rep1

value: untreated


title: RNAseq - MTF2-AID CPs - untreated - rep2


title: RNAseq - SUZ12-AID CPs - auxin - rep1


title: RNAseq - MTF2-AID CPs - untreated - rep1


title: RNAseq - AID-JARID2 CPs - untreated - rep2


title: RB219 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 20

source_name: retinoblastoma sample RB219

value: SAMPLE 76

value: retinoblastoma


title: RB201 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 2

source_name: retinoblastoma sample RB201

value: SAMPLE 58


title: RB217 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 18

source_name: retinoblastoma sample RB217

value: SAMPLE 74


title: RB208 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 9

source_name: retinoblastoma sample RB208

value: SAMPLE 65


title: RB202 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 3

source_name: retinoblastoma sample RB202

value: SAMPLE 59


title: RB216 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 17

source_name: retinoblastoma sample RB216

value: SAMPLE 73


title: RB200 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 1

source_name: retinoblastoma sample RB200

value: SAMPLE 57


title: RB209 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 10

source_name: retinoblastoma sample RB209

value: SAMPLE 66


title: RB206 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 7

source_name: retinoblastoma sample RB206

value: SAMPLE 63


title: RB205 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 6

source_name: retinoblastoma sample RB203

value: SAMPLE 62


title: RB207 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 8

source_name: retinoblastoma sample RB207

value: SAMPLE 64


title: RB204 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 5

source_name: retinoblastoma sample RB21

value: SAMPLE 61


title: RB210 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 11

source_name: retinoblastoma sample RB210

value: SAMPLE 67


title: RB203 (5.3K BAC-CGH)

description:
5.2K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 4

value: SAMPLE 60


title: RNAseq - SUZ12-AID CPs - untreated - rep1

source_name: CPs

value: RNA-seq

value: SUZ12-AID, Tir1


title: RNAseq - SUZ12-AID CPs - untreated - rep2

value: untreated


title: CUT&RUN ESC H3K27me3 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0911

data_processing:
Library strategy: CUT&RUN
Paired-end CUT&RUN reads were aligned the M. musculus mm10 genome using Bowtie2 version 2.3.4.3 (Langmead and Salzberg, 2012) with the --maxins parameter set to 2500, and the --no-unal, --very-sensitive,  and --no-discordant options selected. Duplicated reads were marked using MarkDuplicates with Picard v2.19 (Broad Institute, 2019) and were excluded from downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: A tsv file containing the raw counts summed within a 2.5 kb region up and downstream of all unique RefSeqTSS (n=24667).

source_name: ESCs

growth_protocol: C57BL/6 mouse ESCs (ATCC) were cultured on gelatinized dishes in serum-free N2B27 media  (1:1 mix of neurobasal medium (Gibco) and DMEM/F12 (Gibco), 100 mM MEM nonessential amino acids (Sigma), 55 µM 2-mercaptoethanol (Gibco), 2 mM L-glutamine (Sigma), 0.5% penicillin/streptomycin (Sigma), 1x N27 and 1x B27 (Gibco)) supplemented with 100 U/mL leukemia inhibitory factor (LIF) (Chemicon), 3 µM CHIR99021 (Millipore) and 1 µM PD0325901 (Millipore). Cells were passaged every 2–3 days via dissociation in 0.05% trypsin (Genesee Scientific).

extract_protocol:
CUT&RUN was performed as described online by Meers and Henikoff at https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn. Briefly, cell cultures were harvested, washed and counted with the Countess Automated Cell Counter (Invitrogen). Equal numbers of cells per condition were bound to Concanavalin A-coated magnetic beads (Bangs laboratories), and then permeabilized with 0.015% dig-wash buffer (20 mM HEPES pH 7.5, 150 mM, NaCl, 0.5 mM spermidine, one Roche cOmplete EDTA-free tablet per 50 ml, and 0.015% digitonin). Following bead binding, the supernatant was discarded and the bead-cell slurry was resuspended in 150 µl Antibody buffer (0.015% dig-wash buffer with 2 mM EDTA) containing primary antibody. Antibody incubation was carried out for 2 h at 4 ˚C on a nutator. If needed, bead-cell slurry was further washed with dig-wash buffer and incubated with secondary antibody for an additional hour at 4 ˚C. Samples were washed with Dig-wash buffer to remove unbound antibody, then incubated with Protein A-MNase (700 ng/mL, kind gift of the Sarma lab) in dig-wash buffer for 1 h at 4 ˚C on a nutator. Samples were then washed with dig-wash buffer, resuspended in 100 µL dig-wash buffer and cooled to 0 ˚C on a metal tube rack on ice for 5 min. 2 μL 100 mM CaCl2 was added per sample to activate the MNase, and samples were digested for 30 min at 0 ˚C. The digestion reactions were quenched via addition of 100 μl 2X STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.015% digitonin, 100 ug/mL RNAse A (Thermo Fisher), 50 ug/mL glycoblue (Thermo Fisher), and 100 pg/mL Drosophila S2 spike-in DNA (sonicated to ~200bp). Samples were then incubated for 30 min at 37 ˚C to release CUT&RUN fragments. Supernatant containing CUT&RUN elutions was transferred to fresh tubes and DNA was purified using the MinElute PCR Purification Kit (Qiagen). Purified DNA was quantified using the Qubit dsDNA HS Assay (Thermo Fisher), then used to make sequencing libraries. Paired-end sequencing was performed on a NextSeq 500 (Illumina).
Library preparation began from eluted DNA fragments and proceeded as described above starting with the end-repair step. For both RNAseq and CUT&RUN, paired-end sequencing was performed on a NextSeq 500 (Illumina) with a read length of 38 for read 1 and 38 for read 2.

treatment_protocol: Differentiation to NPCs was performed as follows. ESCs were seeded in serum-free conditions at a density of 15,000 cells/mL and incubated for 12 h to allow for cell attachment. For NPC induction, the ESC media was removed and replaced with N2B27 media supplemented with 40 µg/mL BSA (Sigma) and 10 ng/mL bFGF (R&D Biosystems), and incubated for 72 h with daily media exchanges, then media was replaced with N2B27 media supplemented with 40 µg/mL BSA (Sigma) and 500 nM SAG (Millipore) for an additional 48 h before harvesting for RNA, chromatin, or western blot analysis.

value: untagged, Tir1

tag: epitope

tag: antibody

value: Cell Signaling #9733 (C36B11)


title: CUT&RUN ESC MTF2 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0810

value: Proteintech #16208-1-AP


title: CUT&RUN ESC H3K4me3 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b1012

value: Abcam #ab8580


title: CUT&RUN ESC H3K27me3 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0305


title: CUT&RUN ESC SUZ12 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0608

value: Cell Signaling #3737


title: CUT&RUN ESC JARID2 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0709

value: Bonasio lab (Kaneko et al., 2014)


title: CUT&RUN NPC H3K27me3 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b1010

source_name: NPCs


title: CUT&RUN ESC H3K4me3 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0406


title: CUT&RUN ESC JARID2 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0103


title: CUT&RUN NPC MTF2 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0909


title: CUT&RUN ESC MTF2 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0204


title: CUT&RUN ESC SUZ12 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b1112


title: CUT&RUN NPC H3K4me3 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b1111


title: CUT&RUN NPC IgG - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0606

value: IgG


title: CUT&RUN NPC JARID2 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0808


title: CUT&RUN NPC JARID2 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0202


title: RNAseq - AID-JARID2 NPCs day 0 - untreated - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0206
J2AID.NT.NPC.b2

growth_protocol: C57BL/6 mouse ESCs (ATCC) were cultured on gelatinized dishes in serum-free N2B27 media  (1:1 mix of neurobasal medium (Gibco) and DMEM/F12 (Gibco), 100 mM MEM nonessential amino acids (Sigma), 55 µM 2-mercaptoethanol (Gibco), 2 mM L-glutamine (Sigma), 0.5% penicillin/streptomycin (Sigma), 1x N27 and 1x B27 (Gibco)) supplemented with 100 U/mL leukemia inhibitory factor (LIF) (Chemicon), 3 µM CHIR99021 (Millipore) and 1 µM PD0325901 (Millipore). Cells were passaged every 2–3 days via dissociation in 0.05% trypsin (Genesee Scientific). Differentiation to NPCs was performed as follows. ESCs were seeded in serum-free conditions at a density of 15,000 cells/mL and incubated for 12 h to allow for cell attachment. For NPC induction, the ESC media was removed and replaced with N2B27 media supplemented with 40 µg/mL BSA (Sigma) and 10 ng/mL bFGF (R&D Biosystems), and incubated for 72 h with daily media exchanges, then media was replaced with N2B27 media supplemented with 40 µg/mL BSA (Sigma) and 500 nM SAG (Millipore) for an additional 48 h before harvesting for RNA, chromatin, or western blot analysis.

extract_protocol:
Cells were rinsed once with PBS and lysed via direct addition of TRIzol reagent (Thermo Fisher Scientific). Total cellular RNA was purified using the Direct-zol RNA Miniprep kit (Zymo Research).
PolyA+ RNA was isolated from 500 ng total RNA using Dynabeads Oligo(dT)25 beads (Thermo Fisher) and constructed into strand-specific libraries using the dUTP method. UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter) and quantified by qPCR before and after amplification.

value: AID-JARID2, Tir1

tag: length of treatment

value: 5 days


title: RNAseq - AID-JARID2 NPCs day 0 - auxin - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0308
J2AID.IAA.NPC.b2

value: auxin


title: RNAseq - AID-JARID2 NPCs day 0 - auxin - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0212
J2AID.IAA.NPC.b1


title: CUT&RUN NPC H3K27me3 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0404


title: CUT&RUN NPC MTF2 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0303


title: CUT&RUN NPC SUZ12 - rep2

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0707


title: RNAseq - AID-JARID2 NPCs day 0 - untreated - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0307
J2AID.NT.NPC.b3


title: RNAseq - MTF2-AID NPCs day 0 - auxin - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0311
MAID.IAA.NPC.b2

value: MTF2-AID, Tir1


title: RNAseq - MTF2-AID NPCs day 0 - auxin - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0412
MAID.IAA.NPC.b3


title: CUT&RUN NPC H3K4me3 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0505


title: CUT&RUN NPC SUZ12 - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0101


title: RNAseq - AID-JARID2 NPCs day 0 - auxin - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0409
J2AID.IAA.NPC.b3


title: CUT&RUN ESC IgG - rep1

description:
CUTNRUN.counts.refSeqTSS.tsv
200315.HCF2VBGXF.b0507


title: RNAseq - MTF2-AID NPCs day 0 - untreated - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0612
MAID.NT.NPC.b3


title: RNAseq - MTF2-AID NPCs day 0 - auxin - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0210
MAID.IAA.NPC.b1


title: RNAseq - MTF2-AID NPCs day 0 - untreated - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0511
MAID.NT.NPC.b2


title: RNAseq - SUZ12-AID NPCs day 5 - untreated - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0305
S12AID.NT.NPC.b2


title: RNAseq - SUZ12-AID NPCs day 5 - auxin - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0205
S12AID.IAA.NPC.b2


title: RNAseq - untagged NPCs day 5 - auxin - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0607
B6T1.IAA.NPC.b3


title: RNAseq - untagged NPCs day 5 - auxin - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0506
B6T1.IAA.NPC.b2


title: RNAseq - SUZ12-AID NPCs day 5 - auxin - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0306
S12AID.IAA.NPC.b3


title: RNAseq - AID-JARID2 NPCs day 0 - untreated - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0105
J2AID.NT.NPC.b1


title: RNAseq - SUZ12-AID NPCs day 5 - untreated - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0204
S12AID.NT.NPC.b1


title: RNAseq - AID-JARID2 ESCs day 0 - auxin - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0509
J2AID.IAA.ESC.b2

value: 12 hours


title: RNAseq - untagged NPCs day 5 - untreated - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0808
B6T1.NT.NPC.b2


title: RNAseq - untagged NPCs day 5 - untreated - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0707
B6T1.NT.NPC.b1


title: RNAseq - AID-JARID2 ESCs day 0 - auxin - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0408
J2AID.IAA.ESC.b1


title: RNAseq - MTF2-AID ESCs day 0 - auxin - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0209
MAID.IAA.ESC.b2


title: RNAseq - AID-JARID2 ESCs day 0 - untreated - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0407
J2AID.NT.ESC.b1


title: RNAseq - AID-JARID2 ESCs day 0 - untreated - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0609
J2AID.NT.ESC.b3


title: RNAseq - MTF2-AID ESCs day 0 - untreated - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0712
MAID.NT.ESC.b3


title: RNAseq - untagged NPCs day 5 - auxin - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0405
B6T1.IAA.NPC.b1


title: RNAseq - untagged NPCs day 5 - untreated - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0909
B6T1.NT.NPC.b3


title: RNAseq - AID-JARID2 ESCs day 0 - untreated - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0508
J2AID.NT.ESC.b2


title: RNAseq - MTF2-AID ESCs day 0 - untreated - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0510
MAID.NT.ESC.b1


title: RNAseq - SUZ12-AID NPCs day 5 - untreated - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0406
S12AID.NT.NPC.b3


title: RNAseq - SUZ12-AID ESCs day 0 - auxin - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0709
S12AID.IAA.ESC.b3


title: RNAseq - AID-JARID2 ESCs day 0 - auxin - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0610
J2AID.IAA.ESC.b3


title: RNAseq - MTF2-AID NPCs day 0 - untreated - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0410
MAID.NT.NPC.b1


title: RNAseq - MTF2-AID ESCs day 0 - auxin - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0310
MAID.IAA.ESC.b3


title: RNAseq - SUZ12-AID ESCs day 0 - untreated - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0809
S12AID.NT.ESC.b2


title: RNAseq - SUZ12-AID ESCs day 0 - untreated - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0910
S12AID.NT.ESC.b3


title: RNAseq - SUZ12-AID ESCs day 0 - untreated - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0708
S12AID.NT.ESC.b1


title: RNAseq - untagged ESCs day 0 - auxin - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b1212
B6T1.IAA.ESC.b3


title: RNAseq - untagged ESCs day 0 - auxin - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b1111
B6T1.IAA.ESC.b2


title: RNAseq - MTF2-AID ESCs day 0 - auxin - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0108
MAID.IAA.ESC.b1