title: Patski cells, Rep 2, Day 5, Endogenous targets, 15 nM gRNA

description: Library name: D06

value: Day 5

value: 15 nM endogenous target gRNA


title: Patski cells, Day 1, Target 8-3, 30 nM gRNA

status: Public on Mar 13 2026

type: SRA

city: Pasadena

first: Michael

last: Elowitz

state: CA

address: 1200 E California Blvd

country: USA

institute: Caltech

description: Library name: D38

library_source: genomic

data_processing:
hiPSC and Patski samples were aligned with bwa-mem version 0.7.17-rl188 using default settings.
hiPSC and Patski samples were further processed with custom R scripts to retain bases only at base editor target positions and quantify allele frequencies, as well as filter reads with any target base having quality score less than 10.
Samples D1-6, 13-16, 35, 37-45, 56-65, and 76-85 were processed using Crispresso2 version 2.3.3 using default settings.
Assembly: Custom reference sequences were prepared for each sample based on the expected amplicon(s) for each sample.
Supplementary files format and content: "agg*.txt" processed files contain allele frequency information with columns corresponding to each of the 70 A-to-G base editor targets per read, the total number of reads with that pattern in the "freq" column, and the fractional representation of that read in the sample in the "frac_reads" column.
Supplementary files format and content: "*_Alleles_frequency_table.txt" processed files are the Alleles_frequency_table.txt files output by Crispresso2 by default, containing columns for the aligned read sequence for each allele, the reference sequence, the read frequency, the fractional abundance of the allele, and additional columns as described at https://crispresso2.pinellolab.org/help.

molecule: genomic DNA

organism:
Mus musculus
Mus spretus

source_name: Patski

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue kit forllowing manufacturer instructions.
Libraries were constructed using PCR to generate amplicons of the desired base editable target including Illumina adapter overhangs.

tag: cell line

value: Patski

tag: time

value: Day 1

tag: treatment

value: 30 nM target 8-3 gRNA


title: Tunicamycin 0.04-0.125uM Round-07 (exp420)

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description:
Library name: Tunicamycin 0.04-0.125uM_Round-07 (exp420)
sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
For each round (batch of simultaneously-run screens), read counts for all control samples (untreated, DMSO 0.1%-0.3% or ethanol 0.1%-0.3% treated) were summed together. Read counts for samples that were grown together for part of the 8 days of the screen were also summed together so that each sample represented in the processed data files is independent in terms of genetic drift.
Assembly: sgRNAs from the Extended knock-out (EKO) library (Bertomeu et al. 2017).
Supplementary files format and content: sgrna_read_counts_refseq_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted refSeq gene symbols (January 2016) and updated HGNC gene symbols (2020).
Supplementary files format and content: sgrna_read_counts_exons_and_hypothetical_genes.txt : sgRNA read counts for controls and each independent screen  (sequenced sample experiment numbers are indicated in the colunm headers), targeted exons (hg19 coordinates) and hypothetical genes (AceView or Gencode symbols).
Library strategy: CRISPR Screen

organism: Homo sapiens

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C. Media was changed every two days and cells diluted to 400,000 cells/ml.

extract_protocol:
genomic DNA extracted using the Gentra Puregene kit according to the manufacturer’s instructions (QIAGEN), and sgRNA sequences were PCR-amplified
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 8 days (see Bertomeu et al., 2017 for details). The pooled EKO library was split in different T-75 flasks, compounds added, and propagated for 8 days. Fresh media and compound was added at each cell passage. The untreated control sample with multiple collected time-points was grown in T-175 spinner flasks.

tag: cell type

value: pre-B lymphoid cell line

value: Tunicamycin 0.04uM, then 0.125uM

tag: batch


title: Patski cells, Day 1, Target 8-6, 30 nM gRNA

description: Library name: D41

value: 30 nM target 8-6 gRNA


title: Patski cells, Rep 2, Day 5, Endogenous targets, 30 nM gRNA

description: Library name: D05

value: 30 nM endogenous target gRNA


title: Methotrexate 10nM Round-08 (exp501)

description:
Library name: Methotrexate 10nM_Round-08 (exp501)
sgRNAs PCR-amplified from genomic DNA

value: Methotrexate 10nM


title: No treatment Round-07 (exp428)

description:
Library name: Ctl No treatment D8_Round-07 (exp428)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Q15 1-2uM Round-04 (exp164)

description:
Library name: Q15 1-2uM_Round-04 (exp164)
sgRNAs PCR-amplified from genomic DNA

value: Q15 1, then 2uM


title: GCT_N_235

type: genomic

city: Utrecht

first: Leendert

last: Looijenga

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center

description: Tumor DNA from GCT patient: GCT_N_235

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium MethylationEPIC Beadchip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing:
minfi package in R environment (v4.4.2).
Average beta.

label: Cy3 and Cy5

source_name: Tumor DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the DNeasy Blood & Tissue Kit (69504, Qiagen)

tag: histology

value: YST

tag: Sex

value: Male

tag: location

value: Testis

tag: age

tag: gct type

value: II

tag: material

value: FFPE

tag: disease state

value: Germ cell tumor


title: MK-1775 320nM Round-02 (exp75)

description:
Library name: MK-1775 320nM_Round-02 (exp75)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: GCT_N_259 [2]

description: Tumor DNA from GCT patient: GCT_N_259

value: SE

value: Frozen


title: Ethambutol 25uM Round-08 (exp481)

description:
Library name: Ethambutol 25uM_Round-08 (exp481)
sgRNAs PCR-amplified from genomic DNA

value: Ethambutol 25uM


title: Lenalidomide 20uM Round-07 (exp375)

description:
Library name: Lenalidomide 20uM_Round-07 (exp375)
sgRNAs PCR-amplified from genomic DNA

value: Lenalidomide 20uM


title: GSK-J5 1.5uM Round-08 (exp484)

description:
Library name: GSK-J5 1.5uM_Round-08 (exp484)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: GSK-J5 1.5uM


title: GCT_N_320

description: Tumor DNA from GCT patient: GCT_N_320

value: MIX


title: Dynasore 7uM Round-08 (exp436)

description:
Library name: Dynasore 7uM_Round-08 (exp436)
sgRNAs PCR-amplified from genomic DNA

value: Dynasore 7uM


title: Cyclosporin A 800nM Round-07 (exp347)

description:
Library name: Cyclosporin A 800nM_Round-07 (exp347)
sgRNAs PCR-amplified from genomic DNA

value: Cyclosporin A 800nM


title: Patski cells, Rep 2, Day 3, Endogenous targets, 30 nM gRNA

description: Library name: D03

value: Patski

value: Day 3

value: 30 nM endogenous target gRNA


title: A23187 400nM Round-07 (exp342)

description:
Library name: A23187 400nM_Round-07 (exp342)
sgRNAs PCR-amplified from genomic DNA


title: TGF-beta 44ng/mL Round-08 (exp528)

description:
Library name: TGF-beta 44ng/mL_Round-08 (exp528)
sgRNAs PCR-amplified from genomic DNA

value: TGF-beta 44ng/mL


title: GCT_N_062

description: Tumor DNA from GCT patient: GCT_N_062

value: YST

value: Male

value: Testis

value: I


title: Patski cells, Day 1, Target 8-1, 30 nM gRNA

description: Library name: D35

value: Day 1

value: 30 nM target 8-1 gRNA


title: Patski cells, Rep 2, Day 3, Endogenous targets, 15 nM gRNA

description: Library name: D04

value: 15 nM endogenous target gRNA


title: Spinner flask No treatment Day 4 Round-07 (exp602)

description:
Library name: SF No treatment D4_Round-07 (exp602)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: GCT_N_026

description: Tumor DNA from GCT patient: GCT_N_026

value: Female

value: Ovary

value: FFPE

value: Germ cell tumor


title: N,N-Dimethylsphingosine 2.5uM Round-08 (exp508)

description:
Library name: N,N-Dimethylsphingosine 2.5uM_Round-08 (exp508)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: N,N-Dimethylsphingosine 2.5uM


title: Milciclib 2uM Round-08 (exp502)

description:
Library name: Milciclib 2uM_Round-08 (exp502)
sgRNAs PCR-amplified from genomic DNA

value: Milciclib 2uM


title: Patski cells, Rep 2, Day 1, Endogenous targets, 30 nM gRNA

description: Library name: D01

value: Patski

value: 30 nM endogenous target gRNA


title: GCT_N_322

description: Tumor DNA from GCT patient: GCT_N_322

value: MIX

value: II


title: Patski cells, Day 1, Target 8-5, 30 nM gRNA

description: Library name: D40

value: 30 nM target 8-5 gRNA


title: Cerivastatin 150nM Round-05 (exp226)

description:
Library name: Cerivastatin 150nM_Round-05 (exp226)
sgRNAs PCR-amplified from genomic DNA

value: Cerivastatin 150nM


title: GCT_N_005

description: Tumor DNA from GCT patient: GCT_N_005

value: Male

value: Testis

value: Frozen


title: GCT_N_240 [2]

description: Tumor DNA from GCT patient: GCT_N_240

value: EC


title: Patski cells, Rep 2, Day 1, Endogenous targets, 15 nM gRNA

description: Library name: D02

value: Day 1

value: 15 nM endogenous target gRNA


title: GCT_N_259 [1]

description: Tumor DNA from GCT patient: GCT_N_259


title: Patski cells, Rep 1, Day 3, Endogenous targets, 30 nM gRNA

description: Library name: D15

value: Day 3


title: GCT_N_340

description: Tumor DNA from GCT patient: GCT_N_340

value: FFPE

value: Germ cell tumor


title: Spinner flask No treatment Day 6 Round-09 (exp754)

description:
Library name: SF No treatment D6_Round-09 (exp754)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: No treatment


title: Ibrutinib 1uM Round-07 (exp372)

description:
Library name: Ibrutinib 1uM_Round-07 (exp372)
sgRNAs PCR-amplified from genomic DNA

value: Ibrutinib 1uM


title: GCT_N_240 [1]

description: Tumor DNA from GCT patient: GCT_N_240

value: SE


title: LY2090314 3nM Round-08 (exp499)

description:
Library name: LY2090314 3nM_Round-08 (exp499)
sgRNAs PCR-amplified from genomic DNA


title: Hypoxia 5% O2 D12 Round-04 (exp191)

description:
Library name: Hypoxia 5_ O2_D12_Round-04 (exp191)
sgRNAs PCR-amplified from genomic DNA

value: Hypoxia 5% O2


title: Salinomycin 3.5uM Round-08 (exp521)

description:
Library name: Salinomycin 3.5uM_Round-08 (exp521)
sgRNAs PCR-amplified from genomic DNA

value: Salinomycin 3.5uM


title: No treatment from SF2 Round-08 (exp545)

description:
Library name: Ctl No treatment D8_SF2_Round-08 (exp545)
sgRNAs PCR-amplified from genomic DNA


title: Isoniazid 100uM Round-08 (exp494)

description:
Library name: Isoniazid 100uM_Round-08 (exp494)
sgRNAs PCR-amplified from genomic DNA

value: Isoniazid 100uM


title: Patski cells, Rep 1, Day 3, Endogenous targets, 15 nM gRNA

description: Library name: D16

value: Patski


title: GCT_N_107

description: Tumor DNA from GCT patient: GCT_N_107

value: YST

value: Female

value: Ovary

value: II


title: Patski cells, Day 44, Target Design H10, gRNA H10

description: Library name: Patski89

value: Day 44

value: Target Design H10, gRNA H10


title: DKK1 89ng/mL Round-08 (exp477)

description:
Library name: DKK1 89ng/mL_Round-08 (exp477)
sgRNAs PCR-amplified from genomic DNA

value: DKK1 89ng/mL


title: THZ1 60nM Round-08 (exp531)

description:
Library name: THZ1 60nM_Round-08 (exp531)
sgRNAs PCR-amplified from genomic DNA

value: THZ1 60nM


title: Patski cells, Rep 1, Day 1, Endogenous targets, 30 nM gRNA

description: Library name: D13

value: Day 1

value: 30 nM endogenous target gRNA


title: Myriocin 25uM Round-06 (exp293)

description:
Library name: Myriocin 25uM_Round-06 (exp293)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Myriocin 25uM


title: A-769662 20uM Round-07 (exp331)

description:
Library name: A-769662 20uM_Round-07 (exp331)
sgRNAs PCR-amplified from genomic DNA


title: MS023 2uM Round-03 (exp134)

description:
Library name: MS023 2uM_Round-03 (exp134)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: MS023 2uM


title: GCT_N_307

description: Tumor DNA from GCT patient: GCT_N_307

value: MIX

value: Ovotestis

value: FFPE

value: Germ cell tumor


title: Amiloride 100uM Round-08 (exp447)

description:
Library name: Amiloride 100uM_Round-08 (exp447)
sgRNAs PCR-amplified from genomic DNA

value: Amiloride 100uM


title: Patski cells, Rep 1, Day 1, Endogenous targets, 15 nM gRNA

description: Library name: D14

value: Patski

value: 15 nM endogenous target gRNA


title: Cytochalasin B 5uM Round-07 (exp349)

description:
Library name: Cytochalasin B 5uM_Round-07 (exp349)
sgRNAs PCR-amplified from genomic DNA

value: Cytochalasin B 5uM


title: Day5

type: RNA

city: Tokyo

first: Akihito

last: Ishigami

address: 35-2 Sakae-cho, Itabashi-ku

country: Japan

institute: Tokyo Metropolitan Institute for Geriatrics and Gerontology

description: Gene expression data of newborn rat epidermal keratinocytes induced by RA

hyb_protocol: Samples were hybridized to Clariom™ D Assay, rat (Thermo Fisher Scientific).

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000 7G instrument (Thermo Fisher Scientific),.

data_processing: Raw data were normalized by the signal space transformation robust multichip analysis (SST-RMA) algorithm, and quality checks such as labelling and hybridization were performed using Transcriptome Analysis Console (TAC) v4.0.3 (Thermo Fisher Scientific).

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Labelled cDNA samples were prepared from total RNA using a GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: Newborn rat epidermal keratinocytes (NRK cells) were used in this study. NRK cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Sigma-Aldrich, St. Louis, MO, USA) supplemented with 0.4 µg/mL hydrocortisone (Fujifilm Wako Pure Chemical, Osaka, Japan), 100 units/mL penicillin and 100 µg/mL streptomycin (Gibco, Waltham, MA, USA), and 10% fetal bovine serum (FBS; Serana Europe GmbH, Brandenburg, Germany). Cells were cultured at 37 °C in a humidified atmosphere containing 5% CO₂.

extract_protocol: RNA samples were purified using the RNeasy Mini Kit (QIAGEN, Hilden, Germany).

treatment_protocol: All-trans retinoic acid (Fujifilm Wako Pure Chemical) was dissolved in dimethyl sulfoxide and diluted into 1,000 volumes of the medium just before use.  Cells were treated with 5 µM RA or vehicle control. Medium was replaced every 24 h, and cells were cultured for up to 5 days.

tag: tissue

value: Newborn rat epidermal keratinocytes


title: Patski cells, Day 44, Target Design H05, gRNA H05

description: Library name: Patski85

value: Day 44

value: Target Design H05, gRNA H05


title: Day5RA

source_name: Newborn rat epidermal keratinocytes (NRK cells)


title: Patski cells, Day 44, Target Design H10, gRNA H05

description: Library name: Patski88

value: Target Design H10, gRNA H05


title: Pifithrin-alpha 20uM Round-07 (exp390)

description:
Library name: Pifithrin-alpha 20uM_Round-07 (exp390)
sgRNAs PCR-amplified from genomic DNA

value: Pifithrin-alpha 20uM


title: BI-2536 4.2nM Round-03 (exp95)

description:
Library name: BI-2536 4.2nM_Round-03 (exp95)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: N,N-Diethyl-3-methylbenzamide 500uM Round-08 (exp438)

description:
Library name: N,N-Diethyl-3-methylbenzamide 500uM_Round-08 (exp438)
sgRNAs PCR-amplified from genomic DNA

value: N,N-Diethyl-3-methylbenzamide 500uM


title: Doxorubicin 20nM Round-08 (exp478)

description:
Library name: Doxorubicin 20nM_Round-08 (exp478)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Doxorubicin 20nM


title: CB-839 10uM Round-05 (exp224)

description:
Library name: CB-839 10uM_Round-05 (exp224)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 44, Target Design H10, gRNA H01

description: Library name: Patski87

value: Target Design H10, gRNA H01


title: Ethanol 0.1% Day 8 from SF1 Round-08 (exp542)

description:
Library name: Ctl Ethanol 0.1_ D8_SF1_Round-08 (exp542)
sgRNAs PCR-amplified from genomic DNA

value: Ethanol 0.1%


title: Dihydrosphingosine 8uM Round-08 (exp476)

description:
Library name: Dihydrosphingosine 8uM_Round-08 (exp476)
sgRNAs PCR-amplified from genomic DNA

value: Dihydrosphingosine 8uM


title: HMS-I2 5uM Round-06 (exp287)

description:
Library name: HMS-I2 5uM_Round-06 (exp287)
sgRNAs PCR-amplified from genomic DNA

value: HMS-I2 5uM


title: Patski cells, Day 44, Target Design H05, gRNA H10

description: Library name: Patski86

value: Target Design H05, gRNA H10


title: proboscis, YH1

city: Jinzhong

first: chang

last: song

address: No.1 Mingxian South Road, Taigu District

department: College of Animal Science and Technology

country: China

institute: Shanxi Agricultural University

description: Library name: YH1

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: AcerK1.0
Supplementary files format and content: Excel file includes FPKM values for each Sample

organism: Apis cerana

source_name: proboscis

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: proboscis

tag: group

value: Rapeseed pollen-carrying bees


title: proboscis, YH3

description: Library name: YH3


title: Camptothecin 1nM Round-06 (exp270)

description:
Library name: Camptothecin 1nM_Round-06 (exp270)
sgRNAs PCR-amplified from genomic DNA

value: Camptothecin 1nM


title: Patski cells, Day 44, Target Design H01, gRNA H05

description: Library name: Patski82

value: Patski

value: Target Design H01, gRNA H05


title: Patski cells, Day 44, Target Design H01, gRNA H10

description: Library name: Patski83

value: Day 44

value: Target Design H01, gRNA H10


title: Spinner flask No treatment Day 0 Round-05 (exp588)

description:
Library name: SF No treatment D0_Round-05 (exp588)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Resminostat 500nM Round-07 (exp393)

description:
Library name: Resminostat 500nM_Round-07 (exp393)
sgRNAs PCR-amplified from genomic DNA

value: Resminostat 500nM


title: proboscis, LH2

description: Library name: LH2

value: Pear pollen-carrying bees


title: Phorbol 12-myristate 13-acetate 570nM Round-08 (exp514)

description:
Library name: Phorbol 12-myristate 13-acetate 570nM_Round-08 (exp514)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Phorbol 12-myristate 13-acetate 570nM


title: proboscis, LH1

description: Library name: LH1


title: Patski cells, Day 44, Target Design H05, gRNA H01

description: Library name: Patski84

value: Target Design H05, gRNA H01


title: proboscis, LH3

description: Library name: LH3


title: proboscis, CH3

description: Library name: CH3

value: Non-pollen-carrying bees


title: HMS-I2 1uM Round-06 (exp286)

description:
Library name: HMS-I2 1uM_Round-06 (exp286)
sgRNAs PCR-amplified from genomic DNA

value: HMS-I2 1uM


title: Zebularine 20uM Round-07 (exp423)

description:
Library name: Zebularine 20uM_Round-07 (exp423)
sgRNAs PCR-amplified from genomic DNA

value: Zebularine 20uM


title: Spinner flask No treatment Day 4 Round-04 (exp582)

description:
Library name: SF No treatment D4_Round-04 (exp582)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 41, Target Design H10, gRNA H10

description: Library name: Patski81

value: Day 41

value: Target Design H10, gRNA H10


title: proboscis, YH2

description: Library name: YH2

value: proboscis

value: Rapeseed pollen-carrying bees


title: GSK-J4 1-1.25uM Round-07 (exp363)

description:
Library name: GSK-J4 1-1.25uM_Round-07 (exp363)
sgRNAs PCR-amplified from genomic DNA


title: proboscis, CH2

description: Library name: CH2


title: Patski cells, Day 41, Target Design H10, gRNA H05

description: Library name: Patski80

value: Patski

value: Target Design H10, gRNA H05


title: Patski cells, Day 41, Target Design H10, gRNA H01

description: Library name: Patski79

value: Target Design H10, gRNA H01


title: proboscis, CH1

description: Library name: CH1


title: EST+BAP_4h_3

city: Helsinki

first: Tiina

last: Blomster

address: Viikinkaari 1 (P.O. Box 65)

country: Finland

institute: University of Helsinki

description: Library name: EST+BAP_4h_3

data_processing:
Samples were sequenced with NextSeq 500 ( Illumina) and the raw RNA-seq reads were quality checked using fastqc.
The adapters and barcodes were removed using Trimmomatic [v 0.36].
To align, Kallisto [v.0.43.0] was used, with 4000 bootstrap replicates, to map the high quality reads to Arabidopsis thaliana Reference Transcript Dataset 2 (AtRTD2).
Assembly: Arabidopsis thaliana Reference Transcript Dataset 2 (AtRTD2).
Supplementary files format and content: Tab-separated file includes AGI codes and gene-wise raw count values for each sample.

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Homozygous pANT:XVE>>axr3-1-YFP plants were grown on a nylon mesh (SEFAR NITEX 03-100/44) on vertical plates containing 0.8% Plant Agar (Duchefa), 1% sucrose (Duchefa), 0.5× MS medium including vitamins (Duchefa) and pH adjusted to 5.7–5.8 with 20× MES buffer (Mes monohydrate, Duchefa). The plates were placed in a 23°C growth chamber with long day settings (16 h light and 8 h dark)

extract_protocol:
Total RNA was extracted with the GeneJet Plant RNA purification mini kit (Thermo Scientific). RNA concentrations were measured with NanoDrop 1000 Spectrophotometer and an aliquot was used for RNA quality analysis with Bioanalyzer 2100 (Agilent Technologies).
DNase treatment with Heat&Run gDNA removal kit (ArcticZymes) and ribosomal RNA removal with Plant Ribo-Zero rRNA Removal Kit (Illumina) were done prior to the strand-specific library preparation with a TruSeq Stranded Total RNA Library prep kit (Illumina).

treatment_protocol: For treatment, nine-day-old plants were transferred on the Nitex mesh to plates supplemented with either 5 µM estradiol, 1 µM BAP, 5 µM estradiol and 1 µM BAP or the DMSO control. After 24 hours, 1.5 cm long main main root segments were harvested by cutting the roots 0.5 cm (start) and 2 cm (end) below the root-hypocotyl junction and flash-freezed in liquid N. The experiment was repeated similarly for the 4h time point.

value: root

tag: genotype

value: EST+BAP 4h


title: Spinner flask No treatment Day 6 Round-04 (exp583)

description:
Library name: SF No treatment D6_Round-04 (exp583)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Patski cells, Day 41, Target Design H05, gRNA H10

description: Library name: Patski78

value: Target Design H05, gRNA H10


title: BML-284 90nM Round-08 (exp460)

description:
Library name: BML-284 90nM_Round-08 (exp460)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: UM0131593 200nM Round-03 (exp106)

description:
Library name: UM0131593 200nM_Round-03 (exp106)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: BH1 1uM Round-04 (exp169)

description:
Library name: BH1 1uM_Round-04 (exp169)
sgRNAs PCR-amplified from genomic DNA

value: BH1 1uM


title: Metformin 100-150uM Round-04 (exp170)

description:
Library name: Metformin 100-150uM_Round-04 (exp170)
sgRNAs PCR-amplified from genomic DNA

value: Metformin 100uM, then 150uM


title: Torin1 80nM Round-02 (exp82)

description:
Library name: Torin1 80nM_Round-02 (exp82)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: Torin1 80nM


title: BAP_4h_3

description: Library name: BAP_4h_3

value: BAP 4h


title: Patski cells, Day 41, Target Design H05, gRNA H01

description: Library name: Patski76

value: Target Design H05, gRNA H01


title: MSC2530818 10uM Round-07 (exp379)

description:
Library name: MSC2530818 10uM_Round-07 (exp379)
sgRNAs PCR-amplified from genomic DNA


title: Temozolomide 200uM Round-04 (exp189)

description:
Library name: Temozolomide 200uM_Round-04 (exp189)
sgRNAs PCR-amplified from genomic DNA

value: Temozolomide 200uM


title: BIC1 20uM Round-07 (exp341)

description:
Library name: BIC1 20uM_Round-07 (exp341)
sgRNAs PCR-amplified from genomic DNA

value: BIC1 20uM


title: CCT251545 20uM Round-07 (exp326)

description:
Library name: CCT251545 20uM_Round-07 (exp326)
sgRNAs PCR-amplified from genomic DNA


title: EST_4h_3

description: Library name: EST_4h_3

value: EST 4h


title: Patski cells, Day 41, Target Design H01, gRNA H10

description: Library name: Patski75

value: Day 41

value: Target Design H01, gRNA H10


title: 39oC Round-06 (exp303)

description:
Library name: 39oC_Round-06 (exp303)
sgRNAs PCR-amplified from genomic DNA

value: 39 degrees C


title: DMSO_4h_3

description: Library name: DMSO_4h_3

value: control 4h


title: EST+BAP_4h_2

description: Library name: EST+BAP_4h_2

value: root


title: Patski cells, Day 41, Target Design H05, gRNA H05

description: Library name: Patski77

value: Patski

value: Target Design H05, gRNA H05


title: 2-Methoxyestradiol 550nM Round-07 (exp310)

description:
Library name: 2-Methoxyestradiol 550nM_Round-07 (exp310)
sgRNAs PCR-amplified from genomic DNA

value: 2-Methoxyestradiol 550nM


title: Patski cells, Day 38, Target Design H10, gRNA H10

description: Library name: Patski73

value: Day 38

value: Target Design H10, gRNA H10


title: BAP_4h_2

description: Library name: BAP_4h_2


title: Golgicide A 4uM Round-03 (exp122)

description:
Library name: Golgicide A 4uM_Round-03 (exp122)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Golgicide A 4uM


title: Losmapimod 1uM Round-07 (exp376)

description:
Library name: Losmapimod 1uM_Round-07 (exp376)
sgRNAs PCR-amplified from genomic DNA

value: Losmapimod 1uM


title: EST_4h_2

description: Library name: EST_4h_2


title: Patski cells, Day 38, Target Design H10, gRNA H05

description: Library name: Patski72

value: Target Design H10, gRNA H05


title: Patski cells, Day 41, Target Design H01, gRNA H05

description: Library name: Patski74

value: Target Design H01, gRNA H05


title: Dinaciclib 7nM Round-07 (exp355)

description:
Library name: Dinaciclib 7nM_Round-07 (exp355)
sgRNAs PCR-amplified from genomic DNA

value: Dinaciclib 7nM


title: Bleomycin 5uM Round-08 (exp459)

description:
Library name: Bleomycin 5uM_Round-08 (exp459)
sgRNAs PCR-amplified from genomic DNA

value: Bleomycin 5uM


title: SB743921 1nM Round-05 (exp244)

description:
Library name: SB743921 1nM_Round-05 (exp244)
sgRNAs PCR-amplified from genomic DNA


title: DMSO_4h_2

description: Library name: DMSO_4h_2


title: Patski cells, Day 38, Target Design H05, gRNA H10

description: Library name: Patski70

value: Target Design H05, gRNA H10


title: EST+BAP_4h_1

description: Library name: EST+BAP_4h_1

value: EST+BAP 4h


title: Hydroxyurea 100uM Round-07 (exp329)

description:
Library name: Hydroxyurea 100uM_Round-07 (exp329)
sgRNAs PCR-amplified from genomic DNA

value: Hydroxyurea 100uM


title: Pyronaridine 1uM Round-06 (exp295)

description:
Library name: Pyronaridine 1uM_Round-06 (exp295)
sgRNAs PCR-amplified from genomic DNA

value: Pyronaridine 1uM


title: Patski cells, Day 38, Target Design H10, gRNA H01

description: Library name: Patski71

value: Target Design H10, gRNA H01


title: Atovaquone 15uM Round-08 (exp451)

description:
Library name: Atovaquone 15uM_Round-08 (exp451)
sgRNAs PCR-amplified from genomic DNA

value: Atovaquone 15uM


title: Patski cells, Day 38, Target Design H05, gRNA H05

description: Library name: Patski69

value: Patski

value: Target Design H05, gRNA H05


title: Senexin A 25uM Round-07 (exp400)

description:
Library name: Senexin A 25uM_Round-07 (exp400)
sgRNAs PCR-amplified from genomic DNA

value: Senexin A 25uM


title: PF-06409577 20uM Round-07 (exp389)

description:
Library name: PF-06409577 20uM_Round-07 (exp389)
sgRNAs PCR-amplified from genomic DNA


title: DMSO_4h_1

description: Library name: DMSO_4h_1

value: root

value: control 4h


title: Daidzin 10uM Round-06 (exp280)

description:
Library name: Daidzin 10uM_Round-06 (exp280)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Daidzin 10uM


title: Cidofovir 10uM Round-07 (exp345)

description:
Library name: Cidofovir 10uM_Round-07 (exp345)
sgRNAs PCR-amplified from genomic DNA

value: Cidofovir 10uM


title: CHIR-99021 3.81uM Round-09 (exp697)

description:
Library name: CHIR-99021 3.81uM_Round-09 (exp697)
sgRNAs PCR-amplified from genomic DNA


title: BAP_4h_1

description: Library name: BAP_4h_1

value: BAP 4h


title: Patski cells, Day 35, Target Design H10, gRNA H10

description: Library name: Patski64

value: Day 35

value: Target Design H10, gRNA H10


title: EST_4h_1

description: Library name: EST_4h_1

value: EST 4h


title: D-Fructose 10000uM Round-06 (exp279)

description:
Library name: D-Fructose 10000uM_Round-06 (exp279)
sgRNAs PCR-amplified from genomic DNA

value: D-Fructose 10000uM


title: EST+BAP_24h_3

description: Library name: EST+BAP_24h_3

value: EST+BAP 24h


title: Patski cells, Day 38, Target Design H01, gRNA H05

description: Library name: Patski66

value: Day 38

value: Target Design H01, gRNA H05


title: BI-D1870 2uM Round-04 (exp162)

description:
Library name: BI-D1870 2uM_Round-04 (exp162)
sgRNAs PCR-amplified from genomic DNA


title: Bisphenol S 100uM Round-08 (exp458)

description:
Library name: Bisphenol S 100uM_Round-08 (exp458)
sgRNAs PCR-amplified from genomic DNA

value: Bisphenol S 100uM


title: EST_24h_3

description: Library name: EST_24h_3

value: EST 24h


title: Patski cells, Day 38, Target Design H01, gRNA H10

description: Library name: Patski67

value: Patski

value: Target Design H01, gRNA H10


title: CVT-10216 100nM Round-06 (exp278)

description:
Library name: CVT-10216 100nM_Round-06 (exp278)
sgRNAs PCR-amplified from genomic DNA


title: DMSO_24h_3

description: Library name: DMSO_24h_3

value: root

value: control 24h


title: SAR-020106 2.2uM Round-09 (exp624)

description:
Library name: SAR-020106 2.2uM_Round-09 (exp624)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: Patski cells, Day 35, Target Design H10, gRNA H01

description: Library name: Patski62

value: Target Design H10, gRNA H01


title: CCT251545 200nM Round-06 (exp271)

description:
Library name: CCT251545 200nM_Round-06 (exp271)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 35, Target Design H10, gRNA H05

description: Library name: Patski63

value: Target Design H10, gRNA H05


title: Spinner flask No treatment Day 2 Round-05 (exp589)

description:
Library name: SF No treatment D2_Round-05 (exp589)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Spinner flask No treatment Day 6 Round-05 (exp591)

description:
Library name: SF No treatment D6_Round-05 (exp591)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 38, Target Design H05, gRNA H01

description: Library name: Patski68

value: Target Design H05, gRNA H01


title: L-BMAA 500-750uM Round-04 (exp185)

description:
Library name: L-BMAA 500-750uM_Round-04 (exp185)
sgRNAs PCR-amplified from genomic DNA


title: BAP_24h_3

description: Library name: BAP_24h_3

value: BAP 24h


title: Talazoparib 6nM Round-06 (exp299)

description:
Library name: Talazoparib 6nM_Round-06 (exp299)
sgRNAs PCR-amplified from genomic DNA

value: Talazoparib 6nM


title: Patski cells, Day 35, Target Design H05, gRNA H10

description: Library name: Patski61

value: Day 35

value: Target Design H05, gRNA H10


title: Cannabidiol 20uM Round-08 (exp466)

description:
Library name: Cannabidiol 20uM_Round-08 (exp466)
sgRNAs PCR-amplified from genomic DNA

value: Cannabidiol 20uM


title: Cyclosporin A 3uM Round-07 (exp348)

description:
Library name: Cyclosporin A 3uM_Round-07 (exp348)
sgRNAs PCR-amplified from genomic DNA

value: Cyclosporin A 3uM


title: Patski cells, Day 35, Target Design H05, gRNA H01

description: Library name: Patski59


title: Dexamethasone 0.006-0.015uM Round-07 (exp352)

description:
Library name: Dexamethasone 0.006-0.015uM_Round-07 (exp352)
sgRNAs PCR-amplified from genomic DNA

value: Dexamethasone 0.006uM, then 0.015uM


title: EST+BAP_24h_2

description: Library name: EST+BAP_24h_2

value: EST+BAP 24h


title: Patski cells, Day 35, Target Design H05, gRNA H05

description: Library name: Patski60

value: Patski

value: Target Design H05, gRNA H05


title: VER-155008 3.9uM Round-06 (exp301)

description:
Library name: VER-155008 3.9uM_Round-06 (exp301)
sgRNAs PCR-amplified from genomic DNA


title: DMSO_24h_2

description: Library name: DMSO_24h_2

value: root


title: 2-Methoxyestradiol 0.55-1uM Round-07 (exp312)

description:
Library name: 2-Methoxyestradiol 0.55-1uM_Round-07 (exp312)
sgRNAs PCR-amplified from genomic DNA

value: 2-Methoxyestradiol 0.55uM, then 1uM


title: Patski cells, Day 35, Target Design H01, gRNA H05

description: Library name: Patski57

value: Target Design H01, gRNA H05


title: ABT-702 5uM Round-06 (exp261)

description:
Library name: ABT-702 5uM_Round-06 (exp261)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: ABT-702 5uM


title: BAP_24h_2

description: Library name: BAP_24h_2


title: Patski cells, Day 32, Target Design H10, gRNA H10

description: Library name: Patski56

value: Day 32

value: Target Design H10, gRNA H10


title: Hippuristanol 120nM No dilution on Day 6 Round-08 (exp489)

description:
Library name: Hippuristanol 120nM_No dilution D6_Round-08 (exp489)
sgRNAs PCR-amplified from genomic DNA

value: Hippuristanol 120nM


title: Spinner flask No treatment Day 0 Round-07 (exp600)

description:
Library name: SF No treatment D0_Round-07 (exp600)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: EST_24h_2

description: Library name: EST_24h_2

value: EST 24h


title: LJH685 50uM Round-08 (exp433)

description:
Library name: LJH685 50uM_Round-08 (exp433)
sgRNAs PCR-amplified from genomic DNA

value: LJH685 50uM


title: Patski cells, Day 32, Target Design H10, gRNA H01

description: Library name: Patski54

value: Target Design H10, gRNA H01


title: EST_24h_1

description: Library name: EST_24h_1


title: AICAR 240uM Round-03 (exp116)

description:
Library name: AICAR 240uM_Round-03 (exp116)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: AICAR 240uM


title: EST+BAP_24h_1

description: Library name: EST+BAP_24h_1


title: Ixabepilone 0.004-0.005uM Round-04 (exp184)

description:
Library name: Ixabepilone 0.004-0.005uM_Round-04 (exp184)
sgRNAs PCR-amplified from genomic DNA

value: Ixabepilone 0.004-0.005uM


title: Patski cells, Day 32, Target Design H10, gRNA H05

description: Library name: Patski55

value: Target Design H10, gRNA H05


title: DMSO_24h_1

description: Library name: DMSO_24h_1

value: control 24h


title: Latrunculin B 10uM Round-07 (exp374)

description:
Library name: Latrunculin B 10uM_Round-07 (exp374)
sgRNAs PCR-amplified from genomic DNA

value: Latrunculin B 10uM


title: ML-792 200nM Round-08 (exp505)

description:
Library name: ML-792 200nM_Round-08 (exp505)
sgRNAs PCR-amplified from genomic DNA


title: RO 3306 4.7uM Round-02 (exp80)

description:
Library name: RO 3306 4.7uM_Round-02 (exp80)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: Benzoate 20000uM Round-08 (exp456)

description:
Library name: Benzoate 20000uM_Round-08 (exp456)
sgRNAs PCR-amplified from genomic DNA

value: Benzoate 20000uM


title: BAP_24h_1

description: Library name: BAP_24h_1

value: root

value: BAP 24h


title: PU-H71 1uM Round-08 (exp515)

description:
Library name: PU-H71 1uM_Round-08 (exp515)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: PU-H71 1uM


title: Spinner flask No treatment Day 4 Round-06 (exp596)

description:
Library name: SF No treatment D4_Round-06 (exp596)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 32, Target Design H05, gRNA H05

description: Library name: Patski52

value: Patski

value: Day 32

value: Target Design H05, gRNA H05


title: Calcipotriol 5uM Round-08 (exp464)

description:
Library name: Calcipotriol 5uM_Round-08 (exp464)
sgRNAs PCR-amplified from genomic DNA

value: Calcipotriol 5uM


title: Patski cells, Day 32, Target Design H05, gRNA H10

description: Library name: Patski53

value: Target Design H05, gRNA H10


title: Patski cells, Day 35, Target Design H01, gRNA H10

description: Library name: Patski58

value: Day 35

value: Target Design H01, gRNA H10


title: Zebra finch embryo whole brain E14 heat call female E51

city: Clemson

first: Prakrit

last: Subba

state: SC

address: 132 Long Hall, 230 Parkway Drive

department: Biological Sciences

institute: Clemson University

description:
Library name: E51
Whole brain from E14 zebra finch embryo (E51) exposed to heat call playback (E10–E13, 9h/day); female. EXCLUDED from differential methylation analysis: anomalous bisulfite conversion profile and/or low CpG coverage. Raw data deposited for transparency.

data_processing:
Raw reads were adapter-trimmed and quality-filtered using Trim Galore v0.4.1.
Post-trimming read quality was assessed with FastQC v0.11.5.
Quality-trimmed reads were aligned to the zebra finch reference genome (bTaeGut1.4.pri; NCBI GCF_003957565.2) using BSMAPz v1.1.3 in RRBS mode with MspI site specified (-D C-CGG); only uniquely mapped reads were retained (-r 0).
BAM files from multiple sequencing lanes were merged per sample using samtools merge.
Per-CpG methylation ratios were extracted from merged BAM files using methratio.py (BSMAPz v1.1.3), restricted to CpG context (-x CG), including loci with zero methylation (-z).
Assembly: bTaeGut1.4.pri (NCBI GCF_003957565.2)
Supplementary files format and content: E##_methratio.txt: tab-delimited file containing per-CpG methylation data. Columns: chromosome, position, strand, context, ratio, effective_CT_count, C_count, CT_count, rev_G_count, rev_GA_count, CI_lower, CI_upper.

organism: Taeniopygia guttata

source_name: whole brain

growth_protocol: Fertilized zebra finch (Taeniopygia guttata) eggs were collected on the day of laying and incubated in a fan-less Bellsouth 100 electronic incubator at 37.5°C and 60% relative humidity for nine days (E1–E9).

extract_protocol:
Whole brains were dissected from E14 embryos immediately after decapitation, embedded in OCT compound, flash-frozen on dry ice, and stored at −80°C. Genomic DNA was extracted from whole-brain tissue for RRBS library preparation.
RRBS libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit (NEB E7645S) and NEBNext Multiplex Oligos for Illumina (NEB E7355S) from 300 ng input genomic DNA per sample. Fragments were size-selected to ~250 bp, PCR-amplified for 9 cycles, and assessed by Qubit fluorometer and Agilent 2100 Bioanalyzer. Libraries were enriched for CpG-rich regions by MspI and TaqI digestion and sequenced on an Illumina HiSeq 2000 in 50 bp single-end mode.

treatment_protocol: On E10, eggs were randomly assigned to one of two prenatal acoustic conditions: heat call playback (whine calls + heat calls) or control call playback (whine calls + tet calls). Playback was delivered daily from E10 through E13 for 9 h/day (1000–1900) at 65 dB SPL. On the evening of E13, all embryos were transferred to a shared acoustically silent incubator. On the morning of E14, embryos were euthanized by rapid decapitation.

value: whole brain

value: wild type

value: Female

value: Heat call playback E10–E13


title: DMSO 0.1% Round-04 (exp192)

description:
Library name: Ctl DMSO 0.1_ D8_Round-04 (exp192)
sgRNAs PCR-amplified from genomic DNA

value: DMSO 0.1%


title: GSK461364A 100nM Round-03 (exp126)

description:
Library name: GSK461364A 100nM_Round-03 (exp126)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: Vitamin D3 40uM Round-08 (exp536)

description:
Library name: Vitamin D3 40uM_Round-08 (exp536)
sgRNAs PCR-amplified from genomic DNA

value: Vitamin D3 40uM


title: 2-Methoxyestradiol 0.55-0.75uM Round-07 (exp311)

description:
Library name: 2-Methoxyestradiol 0.55-0.75uM_Round-07 (exp311)
sgRNAs PCR-amplified from genomic DNA

value: 2-Methoxyestradiol 0.55-0.75uM


title: Patski cells, Day 32, Target Design H05, gRNA H01

description: Library name: Patski51

value: Target Design H05, gRNA H01


title: Zebra finch embryo whole brain E14 control call male E49

description:
Library name: E49
Whole brain from E14 zebra finch embryo (E49) exposed to control call playback (E10–E13, 9h/day); male.

value: Male

value: Control call playback E10–E13


title: BI-6727 12.5nM Round-03 (exp97)

description:
Library name: BI-6727 12.5nM_Round-03 (exp97)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: Sulforaphane 9uM Round-08 (exp525)

description:
Library name: Sulforaphane 9uM_Round-08 (exp525)
sgRNAs PCR-amplified from genomic DNA

value: Sulforaphane 9uM


title: Rapamycin 2uM Round-07 (exp306)

description:
Library name: Rapamycin 2uM_Round-07 (exp306)
sgRNAs PCR-amplified from genomic DNA

value: Rapamycin 2uM


title: Zebra finch embryo whole brain E14 heat call female E50

description:
Library name: E50
Whole brain from E14 zebra finch embryo (E50) exposed to heat call playback (E10–E13, 9h/day); female. EXCLUDED from differential methylation analysis: anomalous bisulfite conversion profile and/or low CpG coverage. Raw data deposited for transparency.


title: 3-Bromopyruvate 7uM Round-04 (exp175)

description:
Library name: 3-Bromopyruvate 7uM_Round-04 (exp175)
sgRNAs PCR-amplified from genomic DNA

value: 3-Bromopyruvate 7uM


title: Zebra finch embryo whole brain E14 control call male E45

description:
Library name: E45
Whole brain from E14 zebra finch embryo (E45) exposed to control call playback (E10–E13, 9h/day); male.


title: Nutlin-3A 1.6uM Round-06 (exp294)

description:
Library name: Nutlin-3A 1.6uM_Round-06 (exp294)
sgRNAs PCR-amplified from genomic DNA

value: Nutlin-3A 1.6uM


title: Zebra finch embryo whole brain E14 heat call female E48

description:
Library name: E48
Whole brain from E14 zebra finch embryo (E48) exposed to heat call playback (E10–E13, 9h/day); female.


title: Patski cells, Day 32, Target Design H01, gRNA H05

description: Library name: Patski49

value: Patski

value: Day 32

value: Target Design H01, gRNA H05


title: FTY720 3uM Round-08 (exp483)

description:
Library name: FTY720 3uM_Round-08 (exp483)
sgRNAs PCR-amplified from genomic DNA

value: FTY720 3uM


title: Zebra finch embryo whole brain E14 heat call female E43

description:
Library name: E43
Whole brain from E14 zebra finch embryo (E43) exposed to heat call playback (E10–E13, 9h/day); female. EXCLUDED from differential methylation analysis: anomalous bisulfite conversion profile and/or low CpG coverage. Raw data deposited for transparency.

value: whole brain

value: wild type

value: Female


title: Nicotine 3000uM Round-08 (exp510)

description:
Library name: Nicotine 3000uM_Round-08 (exp510)
sgRNAs PCR-amplified from genomic DNA

value: Nicotine 3000uM


title: Spinner flask No treatment Day 6 Round-06 (exp597)

description:
Library name: SF No treatment D6_Round-06 (exp597)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Patski cells, Day 32, Target Design H01, gRNA H10

description: Library name: Patski50

value: Target Design H01, gRNA H10


title: Patski cells, Day 15, Target Design H10, gRNA H05

description: Library name: Patski44

value: Day 15

value: Target Design H10, gRNA H05


title: Zebra finch embryo whole brain E14 control call female E46

description:
Library name: E46
Whole brain from E14 zebra finch embryo (E46) exposed to control call playback (E10–E13, 9h/day); female.

value: Control call playback E10–E13


title: Vinblastine 15nM Round-05 (exp208)

description:
Library name: Vinblastine 15nM_Round-05 (exp208)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Vinblastine 15nM


title: Patski cells, Day 15, Target Design H05, gRNA none

description: Library name: Patski47

value: Target Design H05, gRNA none


title: Patski cells, Day 15, Target Design H10, gRNA H10

description: Library name: Patski45

value: Target Design H10, gRNA H10


title: Patski cells, Day 15, Target Design H10, gRNA H01

description: Library name: Patski43

value: Patski

value: Target Design H10, gRNA H01


title: Patski cells, Day 15, Target Design H10, gRNA none

description: Library name: Patski48

value: Target Design H10, gRNA none


title: Clomiphene 4.4uM Round-02 (exp68)

description:
Library name: Clomiphene 4.4uM_Round-02 (exp68)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: Clomiphene 4.4uM


title: Wiskostatin 3uM Round-07 (exp422)

description:
Library name: Wiskostatin 3uM_Round-07 (exp422)
sgRNAs PCR-amplified from genomic DNA

value: Wiskostatin 3uM


title: Spinner flask No treatment D1 Round-04 (exp579)

description:
Library name: SF No treatment D1_Round-04 (exp579)
sgRNAs PCR-amplified from genomic DNA


title: Geldanamycin 0.015-0.05uM Round-07 (exp317)

description:
Library name: Geldanamycin 0.015-0.05uM_Round-07 (exp317)
sgRNAs PCR-amplified from genomic DNA

value: Geldanamycin 0.015-0.05uM


title: Spinner flask No treatment D6 Spinner flask 2 Round-08 (exp615)

description:
Library name: SF No treatment D6_SF2_Round-08 (exp615)
sgRNAs PCR-amplified from genomic DNA


title: Zebra finch embryo whole brain E14 control call male E42

description:
Library name: E42
Whole brain from E14 zebra finch embryo (E42) exposed to control call playback (E10–E13, 9h/day); male.

value: whole brain

value: wild type

value: Male


title: Zebra finch embryo whole brain E14 heat call female E47

description:
Library name: E47
Whole brain from E14 zebra finch embryo (E47) exposed to heat call playback (E10–E13, 9h/day); female. EXCLUDED from differential methylation analysis: anomalous bisulfite conversion profile and/or low CpG coverage. Raw data deposited for transparency.

value: Female

value: Heat call playback E10–E13


title: Patski cells, Day 15, Target Design H01, gRNA none

description: Library name: Patski46

value: Day 15

value: Target Design H01, gRNA none


title: Zebra finch embryo whole brain E14 heat call female E41

description:
Library name: E41
Whole brain from E14 zebra finch embryo (E41) exposed to heat call playback (E10–E13, 9h/day); female.


title: BI-6727 40nM Round-03 (exp98)

description:
Library name: BI-6727 40nM_Round-03 (exp98)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: Zebra finch embryo whole brain E14 heat call female E44

description:
Library name: E44
Whole brain from E14 zebra finch embryo (E44) exposed to heat call playback (E10–E13, 9h/day); female. EXCLUDED from differential methylation analysis: anomalous bisulfite conversion profile and/or low CpG coverage. Raw data deposited for transparency.


title: Patski cells, Day 15, Target Design H05, gRNA H10

description: Library name: Patski42

value: Target Design H05, gRNA H10


title: B02 10uM Round-08 (exp453)

description:
Library name: B02 10uM_Round-08 (exp453)
sgRNAs PCR-amplified from genomic DNA


title: Hydroxychloroquine 30uM Round-08 (exp490)

description:
Library name: Hydroxychloroquine 30uM_Round-08 (exp490)
sgRNAs PCR-amplified from genomic DNA

value: Hydroxychloroquine 30uM


title: Quercetin 20uM Round-08 (exp517)

description:
Library name: Quercetin 20uM_Round-08 (exp517)
sgRNAs PCR-amplified from genomic DNA

value: Quercetin 20uM


title: Zebra finch embryo whole brain E14 control call male E40

description:
Library name: E40
Whole brain from E14 zebra finch embryo (E40) exposed to control call playback (E10–E13, 9h/day); male.

value: Control call playback E10–E13


title: Patski cells, Day 15, Target Design H05, gRNA H01

description: Library name: Patski40

value: Patski

value: Target Design H05, gRNA H01


title: Zebra finch embryo whole brain E14 heat call male E39

description:
Library name: E39
Whole brain from E14 zebra finch embryo (E39) exposed to heat call playback (E10–E13, 9h/day); male.


title: Patski cells, Day 15, Target Design H01, gRNA H10

description: Library name: Patski39

value: Target Design H01, gRNA H10


title: UM0131023 50nM Round-05 (exp248)

description:
Library name: UM0131023 50nM_Round-05 (exp248)
sgRNAs PCR-amplified from genomic DNA


title: BI-D1870 3.15uM Round-02 (exp66)

description:
Library name: BI-D1870 3.15uM_Round-02 (exp66)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: BN82002 4uM Round-07 (exp340)

description:
Library name: BN82002 4uM_Round-07 (exp340)
sgRNAs PCR-amplified from genomic DNA


title: DMSO 0.1% Round-06 (exp304)

description:
Library name: Ctl DMSO 0.1_ D8_Round-06 (exp304)
sgRNAs PCR-amplified from genomic DNA

value: DMSO 0.1%


title: Zebra finch embryo whole brain E14 control call male E38

description:
Library name: E38
Whole brain from E14 zebra finch embryo (E38) exposed to control call playback (E10–E13, 9h/day); male.


title: No treatment Round-09 (exp744)

description:
Library name: Ctl No treatment D8_Round-09 (exp744)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Patski cells, Day 15, Target Design H01, gRNA H01

description: Library name: Patski37

value: Target Design H01, gRNA H01


title: Patski cells, Day 15, Target Design H01, gRNA H05

description: Library name: Patski38

value: Target Design H01, gRNA H05


title: Patski cells, Day 12, Target Design H10, gRNA H10

description: Library name: Patski36

value: Day 12

value: Target Design H10, gRNA H10


title: Asunaprevir 3uM Round-07 (exp336)

description:
Library name: Asunaprevir 3uM_Round-07 (exp336)
sgRNAs PCR-amplified from genomic DNA

value: Asunaprevir 3uM


title: Zebra finch embryo whole brain E14 heat call male E35

description:
Library name: E35
Whole brain from E14 zebra finch embryo (E35) exposed to heat call playback (E10–E13, 9h/day); male.

value: whole brain

value: wild type

value: Male

value: Heat call playback E10–E13


title: Zebra finch embryo whole brain E14 control call male E33

description:
Library name: E33
Whole brain from E14 zebra finch embryo (E33) exposed to control call playback (E10–E13, 9h/day); male.


title: Patski cells, Day 12, Target Design H10, gRNA H05

description: Library name: Patski35

value: Target Design H10, gRNA H05


title: Patski cells, Day 15, Target Design H05, gRNA H05

description: Library name: Patski41

value: Day 15

value: Target Design H05, gRNA H05


title: Hinokiflavone 12uM Round-08 (exp487)

description:
Library name: Hinokiflavone 12uM_Round-08 (exp487)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Hinokiflavone 12uM


title: Zebra finch embryo whole brain E14 control call male E36

description:
Library name: E36
Whole brain from E14 zebra finch embryo (E36) exposed to control call playback (E10–E13, 9h/day); male.

value: Control call playback E10–E13


title: Sulforaphane 9uM No dilution on Day 6 Round-08 (exp526)

description:
Library name: Sulforaphane 9uM_No dilution D6_Round-08 (exp526)
sgRNAs PCR-amplified from genomic DNA

value: Sulforaphane 9uM


title: Epigallocatechin gallate 20uM Round-05 (exp230)

description:
Library name: Epigallocatechin gallate 20uM_Round-05 (exp230)
sgRNAs PCR-amplified from genomic DNA

value: Epigallocatechin gallate 20uM


title: Cobalt 18uM Round-07 (exp346)

description:
Library name: Cobalt 18uM_Round-07 (exp346)
sgRNAs PCR-amplified from genomic DNA

value: Cobalt 18uM


title: Zebra finch embryo whole brain E14 control call male E34

description:
Library name: E34
Whole brain from E14 zebra finch embryo (E34) exposed to control call playback (E10–E13, 9h/day); male.


title: Heregulin B 44ng/mL Round-08 (exp486)

description:
Library name: Heregulin B 44ng/mL_Round-08 (exp486)
sgRNAs PCR-amplified from genomic DNA

value: Heregulin B 44ng/mL


title: Patski cells, Day 12, Target Design H10, gRNA H01

description: Library name: Patski34

value: Patski

value: Day 12

value: Target Design H10, gRNA H01


title: IU1-C 25uM Round-04 (exp183)

description:
Library name: IU1-C 25uM_Round-04 (exp183)
sgRNAs PCR-amplified from genomic DNA

value: IU1-C 25uM


title: Zebra finch embryo whole brain E14 heat call female E31

description:
Library name: E31
Whole brain from E14 zebra finch embryo (E31) exposed to heat call playback (E10–E13, 9h/day); female.

value: whole brain

value: wild type

value: Female


title: ABT-702 5uM Deferoxamine 11uM Round-07 (exp321)

description:
Library name: ABT-702 5uM_Deferoxamine 11uM_Round-07 (exp321)
sgRNAs PCR-amplified from genomic DNA

value: ABT-702 5uM and Deferoxamine 11uM


title: Patski cells, Day 12, Target Design H05, gRNA H10

description: Library name: Patski33

value: Target Design H05, gRNA H10


title: BI-2536 20nM Round-03 (exp96)

description:
Library name: BI-2536 20nM_Round-03 (exp96)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: Spinner flask No treatment Day 2 Round-04 (exp580)

description:
Library name: SF No treatment D2_Round-04 (exp580)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: DMSO 0.1% Round-05 (exp250)

description:
Library name: Ctl DMSO 0.1_ D8_Round-05 (exp250)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: DMSO 0.1%


title: Palbociclib 1uM Round-07 (exp382)

description:
Library name: Palbociclib 1uM_Round-07 (exp382)
sgRNAs PCR-amplified from genomic DNA

value: Palbociclib 1uM


title: Thapsigargin 5nM Round-07 (exp407)

description:
Library name: Thapsigargin 5nM_Round-07 (exp407)
sgRNAs PCR-amplified from genomic DNA

value: Thapsigargin 5nM


title: Patski cells, Day 12, Target Design H05, gRNA H05

description: Library name: Patski32

value: Target Design H05, gRNA H05


title: Zebra finch embryo whole brain E14 heat call male E28

description:
Library name: E28
Whole brain from E14 zebra finch embryo (E28) exposed to heat call playback (E10–E13, 9h/day); male.

value: Male

value: Heat call playback E10–E13


title: Radicicol 160nM Round-05 (exp242)

description:
Library name: Radicicol 160nM_Round-05 (exp242)
sgRNAs PCR-amplified from genomic DNA

value: Radicicol 160nM


title: RK-33 8uM Round-08 (exp518)

description:
Library name: RK-33 8uM_Round-08 (exp518)
sgRNAs PCR-amplified from genomic DNA

value: RK-33 8uM


title: Patski cells, Day 12, Target Design H01, gRNA H10

description: Library name: Patski30

value: Patski

value: Day 12

value: Target Design H01, gRNA H10


title: Zebra finch embryo whole brain E14 control call male E32

description:
Library name: E32
Whole brain from E14 zebra finch embryo (E32) exposed to control call playback (E10–E13, 9h/day); male.

value: whole brain

value: wild type

value: Control call playback E10–E13


title: Spinner flask No treatment Day 8 Round-07 (exp604)

description:
Library name: SF No treatment D8_Round-07 (exp604)
sgRNAs PCR-amplified from genomic DNA


title: 2-Deoxy-D-glucose 800uM Round-05 (exp214)

description:
Library name: 2-Deoxy-D-glucose 800uM_Round-05 (exp214)
sgRNAs PCR-amplified from genomic DNA

value: 2-Deoxy-D-glucose 800uM


title: BS-181 20uM Round-08 (exp461)

description:
Library name: BS-181 20uM_Round-08 (exp461)
sgRNAs PCR-amplified from genomic DNA


title: Zebra finch embryo whole brain E14 control call male E27

description:
Library name: E27
Whole brain from E14 zebra finch embryo (E27) exposed to control call playback (E10–E13, 9h/day); male.


title: IU1-47 25uM Round-04 (exp182)

description:
Library name: IU1-47 25uM_Round-04 (exp182)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 12, Target Design H01, gRNA H05

description: Library name: Patski29

value: Target Design H01, gRNA H05


title: Zebra finch embryo whole brain E14 heat call female E29

description:
Library name: E29
Whole brain from E14 zebra finch embryo (E29) exposed to heat call playback (E10–E13, 9h/day); female.

value: Female


title: GSK-J4 1.5uM Round-08 (exp441)

description:
Library name: GSK-J4 1.5uM_Round-08 (exp441)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: GSK-J4 1.5uM


title: Patski cells, Day 12, Target Design H01, gRNA H01

description: Library name: Patski28

value: Target Design H01, gRNA H01


title: CR131-b 5nM Round-08 (exp474)

description:
Library name: CR131-b 5nM_Round-08 (exp474)
sgRNAs PCR-amplified from genomic DNA

value: CR131-b 5nM


title: Zebra finch embryo whole brain E14 heat call male E30

description:
Library name: E30
Whole brain from E14 zebra finch embryo (E30) exposed to heat call playback (E10–E13, 9h/day); male.

value: Male


title: Zebra finch embryo whole brain E14 control call male E26

description:
Library name: E26
Whole brain from E14 zebra finch embryo (E26) exposed to control call playback (E10–E13, 9h/day); male.


title: Zebra finch embryo whole brain E14 heat call female E24

description:
Library name: E24
Whole brain from E14 zebra finch embryo (E24) exposed to heat call playback (E10–E13, 9h/day); female.

value: Heat call playback E10–E13


title: Spinner flask No treatment Day 0 Round-06 (exp594)

description:
Library name: SF No treatment D0_Round-06 (exp594)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Etoposide 300nM Round-05 (exp199)

description:
Library name: Etoposide 300nM_Round-05 (exp199)
sgRNAs PCR-amplified from genomic DNA

value: Etoposide 300nM


title: Zebra finch embryo whole brain E14 control call female E23

description:
Library name: E23
Whole brain from E14 zebra finch embryo (E23) exposed to control call playback (E10–E13, 9h/day); female.


title: TNF-alpha 44ng/mL Round-08 (exp533)

description:
Library name: TNF-alpha 44ng/mL_Round-08 (exp533)
sgRNAs PCR-amplified from genomic DNA

value: TNF-alpha 44ng/mL


title: Patski cells, Day 9, Target Design H10, gRNA H05

description: Library name: Patski26

value: Patski

value: Day 9

value: Target Design H10, gRNA H05


title: DMSO 0.1% from SF1 Round-08 (exp540)

description:
Library name: Ctl DMSO 0.1_ D8_SF1_Round-08 (exp540)
sgRNAs PCR-amplified from genomic DNA

value: DMSO 0.1%


title: Rucaparib 6.5uM Round-08 (exp520)

description:
Library name: Rucaparib 6.5uM_Round-08 (exp520)
sgRNAs PCR-amplified from genomic DNA

value: Rucaparib 6.5uM


title: Zebra finch embryo whole brain E14 heat call male E22

description:
Library name: E22
Whole brain from E14 zebra finch embryo (E22) exposed to heat call playback (E10–E13, 9h/day); male.

value: whole brain

value: wild type


title: Patski cells, Day 12, Target Design H05, gRNA H01

description: Library name: Patski31

value: Day 12

value: Target Design H05, gRNA H01


title: Rapamycin 1nM Round-08 (exp429)

description:
Library name: Rapamycin 1nM_Round-08 (exp429)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Rapamycin 1nM


title: Artemisinin 50uM Round-08 (exp450)

description:
Library name: Artemisinin 50uM_Round-08 (exp450)
sgRNAs PCR-amplified from genomic DNA

value: Artemisinin 50uM


title: Trimetrexate 30nM Round-08 (exp535)

description:
Library name: Trimetrexate 30nM_Round-08 (exp535)
sgRNAs PCR-amplified from genomic DNA

value: Trimetrexate 30nM


title: Patski cells, Day 9, Target Design H10, gRNA H01

description: Library name: Patski25

value: Target Design H10, gRNA H01


title: Patski cells, Day 9, Target Design H05, gRNA H10

description: Library name: Patski24

value: Target Design H05, gRNA H10


title: Patski cells, Day 9, Target Design H10, gRNA H10

description: Library name: Patski27

value: Target Design H10, gRNA H10


title: Zebra finch embryo whole brain E14 control call female E18

description:
Library name: E18
Whole brain from E14 zebra finch embryo (E18) exposed to control call playback (E10–E13, 9h/day); female.

value: Female

value: Control call playback E10–E13


title: UM0130462 0.025-0.035uM Round-05 (exp247)

description:
Library name: UM0130462 0.025-0.035uM_Round-05 (exp247)
sgRNAs PCR-amplified from genomic DNA


title: SNS-032 25uM Round-07 (exp401)

description:
Library name: SNS-032 25uM_Round-07 (exp401)
sgRNAs PCR-amplified from genomic DNA


title: Nifuroxazide 5uM Round-03 (exp102)

description:
Library name: Nifuroxazide 5uM_Round-03 (exp102)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: Nifuroxazide 5uM


title: Zebra finch embryo whole brain E14 control call male E17

description:
Library name: E17
Whole brain from E14 zebra finch embryo (E17) exposed to control call playback (E10–E13, 9h/day); male.

value: Male


title: Patski cells, Day 9, Target Design H05, gRNA H05

description: Library name: Patski23

value: Patski

value: Day 9

value: Target Design H05, gRNA H05


title: Zebra finch embryo whole brain E14 heat call female E19

description:
Library name: E19
Whole brain from E14 zebra finch embryo (E19) exposed to heat call playback (E10–E13, 9h/day); female.

value: whole brain

value: wild type

value: Heat call playback E10–E13


title: proTAME 5uM Round-04 (exp187)

description:
Library name: proTAME 5uM_Round-04 (exp187)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: proTAME 5uM


title: ABT-702 5uM Round-07 (exp318)

description:
Library name: ABT-702 5uM_Round-07 (exp318)
sgRNAs PCR-amplified from genomic DNA

value: ABT-702 5uM


title: Zebra finch embryo whole brain E14 control call male E16

description:
Library name: E16
Whole brain from E14 zebra finch embryo (E16) exposed to control call playback (E10–E13, 9h/day); male.


title: Cytarabine 16nM Round-09 (exp700)

description:
Library name: Cytarabine 16nM_Round-09 (exp700)
sgRNAs PCR-amplified from genomic DNA

value: Cytarabine 16nM


title: Zebra finch embryo whole brain E14 heat call male E15

description:
Library name: E15
Whole brain from E14 zebra finch embryo (E15) exposed to heat call playback (E10–E13, 9h/day); male.


title: Cincreasin 100uM Round-08 (exp473)

description:
Library name: Cincreasin 100uM_Round-08 (exp473)
sgRNAs PCR-amplified from genomic DNA

value: Cincreasin 100uM


title: Hydroxyurea 15uM Round-06 (exp289)

description:
Library name: Hydroxyurea 15uM_Round-06 (exp289)
sgRNAs PCR-amplified from genomic DNA

value: Hydroxyurea 15uM


title: Citral 50uM Round-06 (exp274)

description:
Library name: Citral 50uM_Round-06 (exp274)
sgRNAs PCR-amplified from genomic DNA

value: Citral 50uM


title: Patski cells, Day 9, Target Design H01, gRNA H10

description: Library name: Patski21

value: Target Design H01, gRNA H10


title: Patski cells, Day 9, Target Design H05, gRNA H01

description: Library name: Patski22

value: Target Design H05, gRNA H01


title: Zebra finch embryo whole brain E14 control call male E13

description:
Library name: E13
Whole brain from E14 zebra finch embryo (E13) exposed to control call playback (E10–E13, 9h/day); male.

value: Control call playback E10–E13


title: Patski cells, Day 9, Target Design H01, gRNA H01

description: Library name: Patski19

value: Target Design H01, gRNA H01


title: Patski cells, Day 9, Target Design H01, gRNA H05

description: Library name: Patski20

value: Patski

value: Target Design H01, gRNA H05


title: Zebra finch embryo whole brain E14 heat call male E10

description:
Library name: E10
Whole brain from E14 zebra finch embryo (E10) exposed to heat call playback (E10–E13, 9h/day); male.

value: Male


title: Tretinoin 40uM Round-07 (exp334)

description:
Library name: Tretinoin 40uM_Round-07 (exp334)
sgRNAs PCR-amplified from genomic DNA

value: Tretinoin 40uM


title: 6-Thioguanine 2uM Round-06 (exp259)

description:
Library name: 6-Thioguanine 2uM_Round-06 (exp259)
sgRNAs PCR-amplified from genomic DNA

value: 6-Thioguanine 2uM


title: Paclitaxel 4nM Round-03 (exp103)

description:
Library name: Paclitaxel 4nM_Round-03 (exp103)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: Paclitaxel 4nM


title: Zebra finch embryo whole brain E14 control call female E08

description:
Library name: E08
Whole brain from E14 zebra finch embryo (E08) exposed to control call playback (E10–E13, 9h/day); female.

value: whole brain

value: wild type

value: Female


title: Patski cells, Day 6, Target Design H10, gRNA H05

description: Library name: Patski17

value: Day 6

value: Target Design H10, gRNA H05


title: Resveratrol 16uM Round-03 (exp147)

description:
Library name: Resveratrol 16uM_Round-03 (exp147)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Resveratrol 16uM


title: Etoposide 100nM Round-05 (exp198)

description:
Library name: Etoposide 100nM_Round-05 (exp198)
sgRNAs PCR-amplified from genomic DNA

value: Etoposide 100nM


title: Zebra finch embryo whole brain E14 heat call female E05

description:
Library name: E05
Whole brain from E14 zebra finch embryo (E05) exposed to heat call playback (E10–E13, 9h/day); female.

value: Heat call playback E10–E13


title: Ibrutinib 10uM Round-08 (exp442)

description:
Library name: Ibrutinib 10uM_Round-08 (exp442)
sgRNAs PCR-amplified from genomic DNA

value: Ibrutinib 10uM


title: Spinner flask 1 No treatment Day 0 Round-08 (exp608)

description:
Library name: SF No treatment D0_SF1_Round-08 (exp608)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Spinner flask No treatment D4 Spinner flask 2 Round-08 (exp613)

description:
Library name: SF No treatment D4_SF2_Round-08 (exp613)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 6, Target Design H10, gRNA H01

description: Library name: Patski16

value: Patski

value: Target Design H10, gRNA H01


title: Zebra finch embryo whole brain E14 control call female E03

description:
Library name: E03
Whole brain from E14 zebra finch embryo (E03) exposed to control call playback (E10–E13, 9h/day); female.

value: Control call playback E10–E13


title: Zebra finch embryo whole brain E14 control call female E04

description:
Library name: E04
Whole brain from E14 zebra finch embryo (E04) exposed to control call playback (E10–E13, 9h/day); female.


title: Patski cells, Day 6, Target Design H05, gRNA H10

description: Library name: Patski15

value: Target Design H05, gRNA H10


title: Arsenic trioxide 60uM Round-08 (exp449)

description:
Library name: Arsenic trioxide 60uM_Round-08 (exp449)
sgRNAs PCR-amplified from genomic DNA

value: Arsenic trioxide 60uM


title: CFI-400945 25uM Round-08 (exp469)

description:
Library name: CFI-400945 25uM_Round-08 (exp469)
sgRNAs PCR-amplified from genomic DNA


title: Pomalidomide 20uM Round-07 (exp391)

description:
Library name: Pomalidomide 20uM_Round-07 (exp391)
sgRNAs PCR-amplified from genomic DNA

value: Pomalidomide 20uM


title: Patski cells, Day 6, Target Design H05, gRNA H05

description: Library name: Patski14

value: Target Design H05, gRNA H05


title: Zebra finch embryo whole brain E14 heat call female E01

description:
Library name: E01
Whole brain from E14 zebra finch embryo (E01) exposed to heat call playback (E10–E13, 9h/day); female.

value: whole brain

value: wild type


title: Tunicamycin 40nM Round-07 (exp418)

description:
Library name: Tunicamycin 40nM_Round-07 (exp418)
sgRNAs PCR-amplified from genomic DNA

value: Tunicamycin 40nM


title: Patski cells, Day 6, Target Design H01, gRNA H10

description: Library name: Patski12

value: Day 6

value: Target Design H01, gRNA H10


title: Patski cells, Day 6, Target Design H05, gRNA H01

description: Library name: Patski13

value: Target Design H05, gRNA H01


title: Phenformin 20uM Round-03 (exp143)

description:
Library name: Phenformin 20uM_Round-03 (exp143)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Phenformin 20uM


title: Mitomycin C 60nM Round-08 (exp503)

description:
Library name: Mitomycin C 60nM_Round-08 (exp503)
sgRNAs PCR-amplified from genomic DNA

value: Mitomycin C 60nM


title: Patski cells, Day 6, Target Design H01, gRNA H05

description: Library name: Patski11

value: Target Design H01, gRNA H05


title: JQ1 800nM Round-08 (exp435)

description:
Library name: JQ1 800nM_Round-08 (exp435)
sgRNAs PCR-amplified from genomic DNA

value: JQ1 800nM


title: hiPS cells, Day 23, Target Design H01, gRNA H01

description: Library name: hiPSC04

value: Day 23

value: Target Design H01, gRNA H01


title: hiPS cells, Day 14, Target Design H01, gRNA H01

description: Library name: hiPSC02

value: Day 14


title: hiPS cells, Day 19, Target Design H01, gRNA H01

description: Library name: hiPSC03

value: Day 19


title: YM155 1nM Round-08 (exp432)

description:
Library name: YM155 1nM_Round-08 (exp432)
sgRNAs PCR-amplified from genomic DNA

value: YM155 1nM


title: hiPS cells, Day 9, Target Design H01, gRNA H01

description: Library name: hiPSC01

value: Day 9


title: Cholesterol 3-100nM Round-08 (exp471)

description:
Library name: Cholesterol 3-100nM_Round-08 (exp471)
sgRNAs PCR-amplified from genomic DNA

value: Cholesterol 3-100nM


title: Thalidomide 20uM Round-07 (exp406)

description:
Library name: Thalidomide 20uM_Round-07 (exp406)
sgRNAs PCR-amplified from genomic DNA

value: Thalidomide 20uM


title: Patski cells, Day 6, Target Design H01, gRNA H01

description: Library name: Patski10

value: Patski


title: Bisphenol F 50uM Round-08 (exp457)

description:
Library name: Bisphenol F 50uM_Round-08 (exp457)
sgRNAs PCR-amplified from genomic DNA

value: Bisphenol F 50uM


title: Diepoxybutane 3uM Round-07 (exp354)

description:
Library name: Diepoxybutane 3uM_Round-07 (exp354)
sgRNAs PCR-amplified from genomic DNA

value: Diepoxybutane 3uM


title: Spinner flask 1 No treatment Day 6 Round-08 (exp614)

description:
Library name: SF No treatment D6_SF1_Round-08 (exp614)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Tozasertib 100nM Round-07 (exp414)

description:
Library name: Tozasertib 100nM_Round-07 (exp414)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Tozasertib 100nM


title: LB-100 2uM Round-05 (exp210)

description:
Library name: LB-100 2uM_Round-05 (exp210)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 3, Target Design H10, gRNA H10

description: Library name: Patski09

value: Day 3

value: Target Design H10, gRNA H10


title: Patski cells, Day 3, Target Design H10, gRNA H01

description: Library name: Patski07

value: Target Design H10, gRNA H01


title: Patski cells, Day 6, Target Design H10, gRNA H10

description: Library name: Patski18

value: Day 6


title: Patski cells, Day 3, Target Design H10, gRNA H05

description: Library name: Patski08

value: Target Design H10, gRNA H05


title: Col_7d_DMSO1h_rep2_Alexa488

description:
VIII_9_Cy3_26_Cy5_12_Alexa488.gpr
12

hyb_protocol: The labeled aaRNAs were hybridized with Agilent Arabidopsis gene chips according to manufacturer’s instructions, including 17 hours incubation at 65 degree with 10 rpm rotation.

scan_protocol: Slides were scanned after washing using GenePix 4200 AL (Axon Instruments) with pixel resolution 5µm and line average 2.

data_processing: Image analysis was done using GenePix Pro 6.1, bad spots were manually flagged (flag value -100). Data normalization in R with limma package using local background subtraction NormExp method with offset 50. Quantile-normalized log2-intensities were compared between treatments using linear model with contrasts. Significances were obtained using eBayes method, FDR was used for correcting multiple-testing.

label_protocol: The Cy3, Cy5 and Alexa488 dye coupling with Amino Allyl MessageAmp™ II aRNA Amplification Kit (Life technologies) according to manufacturer’s instructions.

growth_protocol: Col-0 and ipt1,3,5,7 mutants were grown on a nylon mesh (SEFAR NITEX 03-100/44) on vertical plates containing 0.8% Plant Agar (Duchefa), 1% sucrose (Duchefa), 0.5× MS medium including vitamins (Duchefa) and pH adjusted to 5.7–5.8 with 20× MES buffer (Mes monohydrate, Duchefa). 14-day-old Col-0 was grown independently in similar conditions without the mesh

extract_protocol: Total RNA was isolated with Qiagen RNeasy Plant Mini Kit with an on-column DNase treatment.

treatment_protocol: 7-day-old plants were transferred with the mesh to plates containing 1 µM BAP, 1 µM NAA or the respective DMSO control. Samples were harvested after 1, 4, 8 and 24 h post-transfer by cutting primary roots a few millimeters below the hypocotyl, root tips and lateral roots were discarded. From 14-days-old Col-0 the upper main roots were dissected.

value: root


title: Aminopterin 5nM Round-07 (exp335)

description:
Library name: Aminopterin 5nM_Round-07 (exp335)
sgRNAs PCR-amplified from genomic DNA

value: Aminopterin 5nM


title: GSK461364A 5nM Round-03 (exp125)

description:
Library name: GSK461364A 5nM_Round-03 (exp125)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: Dynasore 10uM Round-04 (exp180)

description:
Library name: Dynasore 10uM_Round-04 (exp180)
sgRNAs PCR-amplified from genomic DNA

value: Dynasore 10uM


title: Patski cells, Day 3, Target Design H05, gRNA H10

description: Library name: Patski06

value: Target Design H05, gRNA H10


title: Q15 2.7uM Round-02 (exp79)

description:
Library name: Q15 2.7uM_Round-02 (exp79)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: Spinner flask No treatment Day 8 Round-05 (exp547)

description:
Library name: SF No treatment D8_Round-05 (exp547)
sgRNAs PCR-amplified from genomic DNA


title: Spinner flask No treatment D2 Spinner flask 2 Round-08 (exp611)

description:
Library name: SF No treatment D2_SF2_Round-08 (exp611)
sgRNAs PCR-amplified from genomic DNA


title: Patski cells, Day 3, Target Design H05, gRNA H01

description: Library name: Patski04

value: Target Design H05, gRNA H01


title: ipt_7d_BAP24h_rep1_Cy3

description:
VIII_9_Cy3_26_Cy5_12_Alexa488.gpr
9


title: Rectum_UC_Inflamed [I0380 RSDF00A Xenium5K]

city: Chicago

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

institute: Northwestern University

hyb_protocol: Xenium Human

scan_protocol: Xenium Human

data_processing: We performed cell quality control (QC) on CosMx multi-tissue, Xenium multi-tissue, Xenium colon-specific, CosMx 6K, and Xenium 5K data. For CosMx multi-tissue, we performed QC by removing the cells with fewer than 20 unique molecular identifiers (UMIs). For Xenium multi-tissue and Xenium colon-specific, we performed QC by removing the cells with fewer than 5 UMIs. For CosMx 6K and Xenium 5K data, we performed QC by excluding the cells with fewer than 50 UMIs. After QC, we normalized and transformed the raw datasets using log normalization (each cell’s gene counts are divided by its total counts, multiplied by 10,000, and log transformed). For CosMx 6K and Xenium 5K data, the top 3,000 highly variable genes were next identified. After further scaling the data, we performed principal component analysis on the normalized data and clustered the cells through a shared nearest neighbor approach.

label: Xenium Human Probe Set

source_name: human rectum

label_protocol: Xenium Human

growth_protocol: Colonic biopsies were obtained with informed consent from healthy and IBD patients during routine screening. All procedures were approved by Northwestern University IRB committee (STU00214234) operating under the main biorepository IRB (STU00203172) at the Digestive Health Center. A standardized biopsy collection protocol was used, and biopsies were targeted for the most inflamed portion of each segment, and if no inflammation was present, they were taken from areas adjacent to where routine care biopsies were taken to most closely align with routine care histology assessments.

extract_protocol: Biopsies were immediately placed in formalin jars fixed and transferred to the Northwestern University Pathology Core for automated embedding, cataloging, and H&E imaging. Formalin-fixed, paraffin-embedded blocks were cut into sections on positively charged slides, and full block sections were used for all experiments.

value: rectum


title: Patski cells, Day 3, Target Design H01, gRNA H10

description: Library name: Patski03

value: Patski

value: Target Design H01, gRNA H10


title: A-395 10uM Round-05 (exp218)

description:
Library name: A-395 10uM_Round-05 (exp218)
sgRNAs PCR-amplified from genomic DNA


title: ipt_7d_BAP4h_rep2_Cy5

description:
VII_33_Cy3_15_Cy5_18_Alexa488.gpr
15


title: ipt_7d_NAA4h_rep3_Cy5

description:
VIII_9_Cy3_26_Cy5_12_Alexa488.gpr
26


title: GCT_N_078

description: Tumor DNA from patient GCT_N_078 with GER

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium Methylation 450K Beadchip (Illumina) using standard Illumina protocol.

value: GER

value: Female

value: CNS

value: Unknown

value: II

value: FFPE

value: Germ cell tumor

value: Tumor DNA


title: Col_14d_rep3_Cy3

description:
VII_33_Cy3_15_Cy5_18_Alexa488.gpr
33


title: Patski cells, Day 3, Target Design H01, gRNA H05

description: Library name: Patski02

value: Day 3

value: Target Design H01, gRNA H05


title: ipt_7d_DMSO1h_rep3_Cy5

description:
VI_5_Cy3_21_Cy5_23_Alexa488.gpr
21

value: root


title: Rectum_UC_Inflamed [I0387 RSDF00A Xeniumcolon]


title: Rectum_UC_Noninflamed [I0355 RSDF00A Xenium5K]


title: Patski cells, Day 3, Target Design H01, gRNA H01

description: Library name: Patski01

value: Target Design H01, gRNA H01


title: Spinner flask No treatment D0Spinner flask 2 Round-08 (exp609)

description:
Library name: SF No treatment D0_SF2_Round-08 (exp609)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: No treatment


title: Patski cells, Day 3, Target Design H05, gRNA H05

description: Library name: Patski05

value: Target Design H05, gRNA H05


title: ipt_7d_BAP1h_rep3_Alexa488

description:
VI_5_Cy3_21_Cy5_23_Alexa488.gpr
23


title: Rectum_HC [I0400 RSCF00A Xenium5K]

value: rectum


title: No treatment Round-06 (exp305)

description:
Library name: Ctl No treatment D8_Round-06 (exp305)
sgRNAs PCR-amplified from genomic DNA


title: Rectum_UC_Inflamed [I0387 RSDF00A Xenium5K]


title: Col_14d_rep1_Alexa488

description:
V_13_Cy3_2_Cy5_31_Alexa488.gpr
31


title: GCT_N_318

description: Tumor DNA from patient GCT_N_318 with MIX

value: MIX

value: Male


title: No treatment D8 Spinner flask 1 Round-08 (exp544)

description:
Library name: Ctl No treatment D8_SF1_Round-08 (exp544)
sgRNAs PCR-amplified from genomic DNA


title: Rectum_UC_Noninflamed [I0355 RSDF00A Xeniumcolon]


title: LB-100 4.1uM Round-02 (exp72)

description:
Library name: LB-100 4.1uM_Round-02 (exp72)
Illumina HiSeq 2000, sgRNAs PCR-amplified from genomic DNA


title: Rectum_HC [I0400 RSCF00A Xeniumcolon]


title: Rectum_UC_Inflamed [I0380 RSDF00A Xeniumcolon]


title: GCT_N_317

description: Tumor DNA from patient GCT_N_317 with MIX

value: Female


title: ipt_7d_BAP8h_rep2_Alexa488

description:
VII_33_Cy3_15_Cy5_18_Alexa488.gpr
18


title: Rectum_UC_Inflamed [I0387 RSDF00A WS Xenium337]


title: TIC10 10uM Round-08 (exp532)

description:
Library name: TIC10 10uM_Round-08 (exp532)
sgRNAs PCR-amplified from genomic DNA

value: TIC10 10uM


title: GCT_N_074

description: Tumor DNA from patient GCT_N_074 with GER

value: GER

value: CNS

value: Unknown


title: N,N-Diethyl-3-methylbenzamide 100uM Round-05 (exp237)

description:
Library name: N,N-Diethyl-3-methylbenzamide 100uM_Round-05 (exp237)
sgRNAs PCR-amplified from genomic DNA

value: N,N-Diethyl-3-methylbenzamide 100uM


title: GCT_N_077

description: Tumor DNA from patient GCT_N_077 with GER

value: II

value: FFPE

value: Germ cell tumor

value: Tumor DNA


title: Rectum_UC_Inflamed [I0380 RSDF00A WS Xenium337]


title: GCT_N_076

description: Tumor DNA from patient GCT_N_076 with TE

value: TE


title: Cryptotanshinone 12uM Round-05 (exp227)

description:
Library name: Cryptotanshinone 12uM_Round-05 (exp227)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Cryptotanshinone 12uM


title: ipt_7d_BAP4h_rep1_Cy3

description:
VI_5_Cy3_21_Cy5_23_Alexa488.gpr
5

value: root


title: Rectum_HC [I0400 RSCF00A WS Xenium337]

value: rectum


title: GCT_N_075

description: Tumor DNA from patient GCT_N_075 with TE


title: Dimethyloxaloylglycine 11uM Round-07 (exp314)

description:
Library name: Dimethyloxaloylglycine 11uM_Round-07 (exp314)
sgRNAs PCR-amplified from genomic DNA

value: Dimethyloxaloylglycine 11uM


title: Spinner flask 2 No treatment Day 8 Round-08 (exp617)

description:
Library name: SF No treatment D8_SF2_Round-08 (exp617)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Rectum_UC_Noninflamed [I0355 RSDF00A WS Xenium337]


title: MK2206 4uM Round-08 (exp504)

description:
Library name: MK2206 4uM_Round-08 (exp504)
sgRNAs PCR-amplified from genomic DNA


title: Curcumin 6.5uM Round-06 (exp277)

description:
Library name: Curcumin 6.5uM_Round-06 (exp277)
sgRNAs PCR-amplified from genomic DNA

value: Curcumin 6.5uM


title: Col_7d_DMSO1h_rep3_Cy3

description:
IV_3_Cy5_19_Alexa488_22_Cy3.gpr
22


title: GCT_N_073

description: Tumor DNA from patient GCT_N_073 with GER

value: Female


title: ipt_7d_BAP24h_rep2_Alexa488

description:
IV_3_Cy5_19_Alexa488_22_Cy3.gpr
19


title: Rectum_UC_Inflamed [I0387 RSDF00A NS Xenium337]


title: Col_7d_DMSO1h_rep1_Cy5

description:
V_13_Cy3_2_Cy5_31_Alexa488.gpr
2


title: ipt_7d_BAP4h_rep3_Alexa488

description:
III_8_Cy5_16_Cy3_25_Alexa488.gpr
25


title: UM0011500 10uM Round-05 (exp246)

description:
Library name: UM0011500 10uM_Round-05 (exp246)
sgRNAs PCR-amplified from genomic DNA


title: ipt_7d_BAP1h_rep2_Cy3

description:
V_13_Cy3_2_Cy5_31_Alexa488.gpr
13


title: Rectum_UC_Inflamed [I0380 RSDF00A NS Xenium337]


title: ipt_7d_BAP1h_rep1_Cy5

description:
IV_3_Cy5_19_Alexa488_22_Cy3.gpr
3


title: GCT_N_072

description: Tumor DNA from patient GCT_N_072 with TE

value: Male


title: Dimethyloxaloylglycine 100uM Round-05 (exp229)

description:
Library name: Dimethyloxaloylglycine 100uM_Round-05 (exp229)
sgRNAs PCR-amplified from genomic DNA

value: Dimethyloxaloylglycine 100uM


title: GCT_N_071

description: Tumor DNA from patient GCT_N_071 with TE

value: CNS

value: Unknown


title: ipt_7d_NAA4h_rep2_Cy3

description:
III_8_Cy5_16_Cy3_25_Alexa488.gpr
16


title: Deferoxamine 11uM Round-07 (exp350)

description:
Library name: Deferoxamine 11uM_Round-07 (exp350)
sgRNAs PCR-amplified from genomic DNA

value: Deferoxamine 11uM


title: ipt_7d_BAP8h_rep1_Cy5

description:
III_8_Cy5_16_Cy3_25_Alexa488.gpr
8


title: GCT_N_067

description: Tumor DNA from patient GCT_N_067 with GER

value: GER

value: II

value: FFPE


title: Rectum_UC_Noninflamed [I0355 RSDF00A NS Xenium337]


title: Ribavirin 10-15uM Round-04 (exp160)

description:
Library name: Ribavirin 10-15uM_Round-04 (exp160)
sgRNAs PCR-amplified from genomic DNA

value: Ribavirin 10uM, then 15uM


title: GCT_N_069

description: Tumor DNA from patient GCT_N_069 with GER

value: Germ cell tumor

value: Tumor DNA


title: Chloroquine 32uM Round-08 (exp470)

description:
Library name: Chloroquine 32uM_Round-08 (exp470)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Chloroquine 32uM


title: Rectum_UC_Noninflamed [I0276 RSDF00A Xenium337]

value: rectum


title: Rectum_HC [I0400 RSCF00A NS Xenium337]


title: Col_14d_rep2_Cy5

description:
II_1_Cy3_6_Alexa488_32_Cy5.gpr
32

value: root


title: No treatment Round-05 (exp252)

description:
Library name: Ctl No treatment D8_Round-05 (exp252)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: GCT_N_066

description: Tumor DNA from patient GCT_N_066 with GER

value: Female


title: Rectum_UC_Inflamed [I0284 RSDF00A Xenium337]


title: GCT_N_070

description: Tumor DNA from patient GCT_N_070 with GER


title: Cisplatin 350nM Round-06 (exp273)

description:
Library name: Cisplatin 350nM_Round-06 (exp273)
sgRNAs PCR-amplified from genomic DNA

value: Cisplatin 350nM


title: ipt_7d_BAP24h_rep3_Cy5

description:
I_11_Alexa488_28_Cy3_29_Cy5.gpr
29


title: Rectum_UC_Inflamed [I0321 RSDF00A Xenium337]


title: ipt_7d_NAA4h_rep1_Alexa488

description:
II_1_Cy3_6_Alexa488_32_Cy5.gpr
6


title: Mouse Testis, Dnmt3l KO_2 P8 (rep 2)

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

description:
Library name: Sample 6
column name in TE_read_count.csv and TE_TMM.csv: P8_Dnmt3lKO_2

data_processing:
Raw reads were loaded to cutadapt v1.13 to trim 3' adaptro, and only reads with length between 18-45 nt would be kep. Trimmed reads were further examined for the sequencing quality via FastQC v0.10.1 and mapped to GENCODE GRCm39 whole genome using TopHat v2.1.1 with parameters "-g 1 -N 0 --read-gap-length 0 --read-edit-dist 0 --read-realign-edit-dist 0 --max-insertion-length 0 --max-deletion-length 0".
Known rRNA, tRNA, and miRNA regions from RNAcentral (https://rnacentral.org) were considered not piRNA candidates and removed during preprocessing. Specificaaly, Bowtie v1.1.1 was used to filter out rRNA and tRNA based on Rfam, and to exclude known and novel (predicted) miRNAs annotated in miRBase and miRDeep2, respectively. Reads of 24-34 nt in length were retained as piRNA candidates.
Potential eRNA-producing regions were taken by extending the TSSs listed in eRNAbase wild-type or primary culture samples by 500 nt in both directions. eRNA regions were collapased using bedtools merge operation, grouped by tissue or cell types, and taken strand into account using the "-s -c 6 -o distinct" parameters.
Mutant VS control piRNA-eRNA association comparisons were done the same way as with enhancers.
Assembly: GRCm39
Supplementary files format and content: CSV  files include raw read counts as well as TMM-normalized values for each Sample.

organism: Mus musculus

source_name: Testis

extract_protocol:
Postnatal SPCs were isolated from enriched germ cells at 0 ddp and from THy1+ SSC-eriched populations at 8 dpp. Total RNAs were extracted using Ambion Tri-Reagent, and small RNAs (15-36 nucleotides) were purified by PAGE fractionation.
Library construction was performed using illumina small RNA sample preparation kit and sequenced via Illumina HiSeq 2000.

treatment_protocol: Examination of wild-type and Dnmt3l knockout smaples in postnatal male germ cells.

value: Testis

value: Spermatogonia

tag: strain

value: Dnmt3l Knockout

value: Postnatal Day 8


title: Rectum_UC_Inflamed [I0277 RSDF00A Xenium337]


title: GCT_N_068

description: Tumor DNA from patient GCT_N_068 with GER

value: GER

value: Male

value: CNS

value: Unknown


title: Rectum_UC_Inflamed [I0286 RSDF00A Xenium337]


title: IWR-1-endo 50uM Round-08 (exp495)

description:
Library name: IWR-1-endo 50uM_Round-08 (exp495)
sgRNAs PCR-amplified from genomic DNA

value: IWR-1-endo 50uM


title: Cabazitaxel 1nM Round-05 (exp223)

description:
Library name: Cabazitaxel 1nM_Round-05 (exp223)
sgRNAs PCR-amplified from genomic DNA

value: Cabazitaxel 1nM


title: GCT_N_327

description: Tumor DNA from patient GCT_N_327 with MIX

value: MIX

value: Ovary

value: II

value: Frozen

value: Germ cell tumor

value: Tumor DNA


title: Rectum_UC_Noninflamed [I0310 RSDF00A Xenium337]

value: rectum


title: Cyclic AMP 200uM Round-08 (exp475)

description:
Library name: Cyclic AMP 200uM_Round-08 (exp475)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line

value: Cyclic AMP 200uM


title: GCT_N_042

description: Tumor DNA from patient GCT_N_042 with TE

value: TE

value: Testis

value: I


title: Mouse Testis, Dnmt3l WT_2 P8 (rep 2)

description:
Library name: Sample 4
column name in TE_read_count.csv and TE_TMM.csv: P8_WT_2

value: Spermatogonia

value: Wild Type

value: Postnatal Day 8


title: ipt_7d_BAP8h_rep3_Cy3

description:
I_11_Alexa488_28_Cy3_29_Cy5.gpr
28

value: root


title: GCT_N_159

description: Tumor DNA from patient GCT_N_159 with SE

value: SE

value: Male


title: GCT_N_039

description: Tumor DNA from patient GCT_N_039 with TE

value: Female

value: Sacrum


title: ipt_7d_DMSO1h_rep1_Cy3

description:
II_1_Cy3_6_Alexa488_32_Cy5.gpr
1


title: Delta-9-Tetrahydrocannabinol 30uM Round-08 (exp445)

description:
Library name: Delta-9-Tetrahydrocannabinol 30uM_Round-08 (exp445)
sgRNAs PCR-amplified from genomic DNA

value: Delta-9-Tetrahydrocannabinol 30uM


title: Rectum_CD_Noninflamed [I0294 RSDF00A Xenium337]


title: Mouse Testis, Dnmt3l KO P0

description:
Library name: Sample 2
column name in TE_read_count.csv and TE_TMM.csv: P0_Dnmt3lKO

value: Dnmt3l Knockout

value: Postnatal Day 0


title: Ileum_UC_Noninflamed [I0321 ITDF00A Xenium337]

source_name: human Ileum

value: Ileum


title: Ileum_UC_Noninflamed [I0310 ITDF00A Xenium337]


title: GCT_N_043

description: Tumor DNA from patient GCT_N_043 with TE

value: Frozen

value: Germ cell tumor

value: Tumor DNA


title: NMS-873 70nM Round-07 (exp380)

description:
Library name: NMS-873 70nM_Round-07 (exp380)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: Mouse Testis, Dnmt3l KO_1 P8 (rep 1)

description:
Library name: Sample 5
column name in TE_read_count.csv and TE_TMM.csv: P8_Dnmt3lKO_1

value: Testis


title: Mouse Testis, Dnmt3l WT_1 P8 (rep 1)

description:
Library name: Sample 3
column name in TE_read_count.csv and TE_TMM.csv: P8_WT_1

value: Spermatogonia


title: GCT_N_044

description: Tumor DNA from patient GCT_N_044 with TE

value: TE

value: Mediastinum

value: I


title: ipt_7d_DMSO1h_rep2_Alexa488

description:
I_11_Alexa488_28_Cy3_29_Cy5.gpr
11

value: root


title: Rectum_CD_Noninflamed [I0275 RSDF00A Xenium337]

value: rectum


title: Spinner flask 1 No treatment D4 Round-08 (exp612)

description:
Library name: SF No treatment D4_SF1_Round-08 (exp612)
sgRNAs PCR-amplified from genomic DNA

value: No treatment


title: Mouse Testis, Dnmt3l WT P0

description:
Library name: Sample 1
column name in TE_read_count.csv and TE_TMM.csv: P0_WT

value: Wild Type


title: GCT_N_038

description: Tumor DNA from patient GCT_N_038 with TE

value: Female

value: Ovary


title: Docosahexaenoic acid 50uM Round-07 (exp356)

description:
Library name: Docosahexaenoic acid 50uM_Round-07 (exp356)
sgRNAs PCR-amplified from genomic DNA

value: Docosahexaenoic acid 50uM


title: GCT_N_037

description: Tumor DNA from patient GCT_N_037 with TE

value: Sacrum


title: Rectum_CD_Inflamed [I0262 RSDF00A Xenium337]


title: Rectum_CD_Inflamed [I0303 RSDF00A Xenium337]


title: iPSC_MG_TREM2_mut (TREM2) timepoint 28 rep 1

city: Zurich

first: Izaskun

last: Mallona

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: Library name: 20220504.B-TREM2-A1_1_R1

data_processing:
RNA-seq raw reads were processed using ARMOR (PMC6643886). Reads were aligned and counted against the human genome GRCh38 assembly and Gencode release 43 annotation using salmon v1.4.0 and STAR 2.7.7a.
Assembly: GRCh38
Supplementary files format and content: shiny_sce.rds
Supplementary files format and content: R (SingleCellExperiment) RDS file, to be read with `readRDS()` in base R. Even if these data are bulk RNA-seq, it makes use of the SingleCellExperiment class. It contains two SingleCellExperiment objects generated using the ARMOR RNA‑seq workflow: one at the transcript level and one at the gene level. The transcript‑level object (sce_tx) includes 111,002 transcripts across 13 samples, with assays for raw counts, transcript abundances, and effective lengths. Row metadata contains transcript and gene identifiers as well as gene symbols and names. Sample‑level metadata includes sample name, type, treatment group, batch, mutation status, and timepoint.  The gene‑level object (sce_gene) contains 20,337 genes across the same 13 samples, with assays for raw counts, abundances, effective lengths, and log‑CPM values computed via edgeR. Row metadata includes gene identifiers, associated transcript IDs, gene symbols and names, and differential expression statistics produced by ARMOR/edgeR for the experimental contrasts (mainly mutants vs WT). Sample metadata is identical to that of the transcript‑level object. All samples correspond to iPSC‑derived microglia, including wild‑type controls and mutant lines for Slc37a2 and TREM2, processed in this analysis in a single batch.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from mature iMGL (1*106 cells) using both the RNeasy Micro kit (Qiagen) or the Direct-zol RNA miniprep (Zymo Research), according to the manufacturers’ protocols. The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed.
The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Fragment Analyzer (Agilent, Santa Clara, California, USA).  The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.

value: day 28


title: iPSC_MG_TREM2_mut (TREM2) timepoint 28 rep 2

description: Library name: 20220504.B-TREM2-A1_2_R1


title: GCT_N_034

description: Tumor DNA from patient GCT_N_034 with TE

value: Male

value: Frozen

value: Germ cell tumor


title: UM0011500 5uM Round-05 (exp245)

description:
Library name: UM0011500 5uM_Round-05 (exp245)
sgRNAs PCR-amplified from genomic DNA

value: pre-B lymphoid cell line


title: iPSC_MG_Slc37a2_mut2 (Slc37a2) timepoint 28 rep 2

description: Library name: 20220504.B-SLC-EX6C5_2_R1


title: Ileum_CD_Inflamed [I0275 ITDF00A Xenium337]

value: Ileum


title: Betulinic acid 10-15uM Round-05 (exp222)

description:
Library name: Betulinic acid 10-15uM_Round-05 (exp222)
sgRNAs PCR-amplified from genomic DNA

value: Betulinic acid 10uM, then 15uM


title: GCT_N_018

description: Tumor DNA from patient GCT_N_018 with TE

value: TE

value: Tumor DNA


title: GCT_N_017

description: Tumor DNA from patient GCT_N_017 with TE

value: I


title: IL-3 9ng/mL Round-08 (exp493)

description:
Library name: IL-3 9ng/mL_Round-08 (exp493)
sgRNAs PCR-amplified from genomic DNA

value: IL-3 9ng/mL


title: GCT_N_032

description: Tumor DNA from patient GCT_N_032 with TE

value: Mediastinum


title: Ileum_CD_Noninflamed [I0278 ITDF00A Xenium337]