title: lung alveolar organoid, Map2k3 knockout, plate3-2 well D09

description: Library name: 3-2_D09_MAP2K3

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Map2k3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Elovl1 knockout, plate3-2 well D08

status: Public on Jun 26 2026

type: SRA

city: South San Francisco

first: Anne

last: Biton

state: CA

address: 1 DNA way

country: USA

institute: Genentech

description: Library name: 3-2_D08_ELOVL1

library_source: transcriptomic

data_processing:
The sequencing reads in each fastq file were first split between mouse and human using Xenome (Conway et al., 2012). Only reads unambiguously assigned to either mouse or human were kept and respectively aligned to their reference genome (mouse: GRCm38.p5, human: GRCh38.p10) through the HTSeqGenie v4.35 Bioconductor package (Pau and Reeder, 2012, https://doi.org/10.18129/B9.bioc.HTSeqGenie). First, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. Then, reads were aligned using GSNAP (Wu et al., 2010; Wu et al., 2016) version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes database (human: GENCODE 27, mouse: GENCODE M15). Reads unambiguously mapping to exons were counted to get gene-level read counts.
Assembly: GRCm38.p5, GRCh38.p10
Supplementary files format and content: gene_counts.xlsx provides gene-level counts of reads unambiguously mapping to exons. There is one table for the reads assigned by Xenome to the Mus Musculus genome (originating from the mouse alveolar type 2 cells of the organoids in the well), and one table for the reads assigned to the Homo Sapiens genome (originating from the human fibroblasts of the organoids in the well).
Supplementary files format and content: plate_design.csv contains the sgRNA sequences used to target each gene and their location on the four plates.
Supplementary files format and content: imaging_outputs.csv contains the main outputs of the image analysis performed on each well at day 7 and day 14, in terms of number or organoids in the well, average area of the organoids in the well, and estimate of the percentage of the well covered by organoids.
Supplementary files format and content: xenome_stats.csv contains the summary of the sequencing read assignment made by Xenome (Conway et al., 2012).

molecule: total RNA

organism:
Homo sapiens
Mus musculus

source_name: lung mouse alveolar type 2 cells and primary human fibroblasts

extract_protocol:
Libraries were prepared from extracted RNA using a modified Smart-seq3 protocol ( Hagemann-Jensen, M., Ziegenhain, C., Chen, P. et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat Biotechnol 38, 708–714 (2020). https://doi.org/10.1038/s41587-020-0497-0) Annealing reaction was performed with 4ul purified RNA, 0.8 ul 40% PEG 8000, 0.08 ul RNAse Inhibitor, 0.04 ul Smart-seq3 oligo dT (100µM), 0.3 ul dNTP (25mM each) and 1 ul water per 384 well reaction. 10 ul mineral oil was added on top to prevent evaporation. Reaction was sealed, spun and incubated at 70˚C for 10 min. Reverse translation was performed by adding 2 ul of RT mix (0.2ul Tris HCl, pH8.0 (1M), 0.24 ul NaCl (1M), 0.2 ul MgCl2 (100mM), 0.08 ul GTP (10mM), 0.64 ul DTT (100mM), 0.16 ul TSO (100µM), 0.08 ul Maxima H Minus RTase and 0.4 ul water) to each 384 well reaction. The RT reaction was incubated at 42°C for 90 min and repeated the following steps for 10 cycles: 50˚C for 2 min and 42˚C for 2 min, and was terminated at 85°C for 5 min.
cDNA amplification was performed by adding 12ul of PCR mix (0.1 ul cDNA fwd (100µM), 0.02 ul cDNA rev (100µM), 0.1 ul MgCl2 (100mM), 10 ul 2X Kapa HiFi Hotstart Readymix  and 1.78 ul water) to the RT reaction for a total of 20 ul. Reaction was thermal cycled at 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 4 min] x 14 cycles, 72 °C 4min. cDNA was diluted 1:10 in water. 1 ul of each sample was transferred to a new 384 well plate to perform tagmentation. 3 ul of tagmentation mix (0.8 ul 5X TAPS Mg buffer, 0.1 ul Tn5 enzyme, 2.1 ul water) was added to each sample on ice. Plate was sealed, vortexed for 15 seconds and spun. The reaction mixture was incubated at 55 °C for 10 min. Reaction was quenched by adding 0.5µl of 0.2% SDS to each well, sealing, vortexing for 15 seconds, and spinning the plate. The plate was  incubated at room temperature for 5 min. Libraries were indexed by added 3.5 ul of PCR mix and 2 ul indexing primers  to each sample.  Reaction was thermal cycled at 72°C for 5 min, 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 30 sec] x 10 cycles, 72 °C 4min. Libraries were pooled and sequenced on an Illumina NovaSeq X Plus system, targeting 8M reads per library.

tag: cell type

tag: genotype

value: Elovl1 CRISPR/Cas9 knockout

tag: batch


title: breast cancer_MD127_S

type: RNA

city: Houston

first: William

middle: Fraser

last: Symmans

state: TX

address: 2130 W Holcombe Blvd #11.4000

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 600 breast cancer specific genes.

label: biotin

organism: Homo sapiens

source_name: breast cancer sample

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

treatment_protocol: Patients consented to future tissue-based research sample collections from either prospective biopsy or surgical resection.

tag: er status

value: P

tag: pr status

value: L

tag: her2 status

value: N

tag: ajcc stage

value: IIA

tag: sample collection type

value: Tissue

tag: setting of sample collection

value: Surgical Tissue Sample


title: breast cancer_MD59_S

value: IIB


title: lung alveolar organoid, Tigit knockout, plate3-2 well D07

description: Library name: 3-2_D07_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_MD43_S


title: lung alveolar organoid, Ank3 knockout, plate3-2 well D06

description: Library name: 3-2_D06_ANK3

value: Ank3 CRISPR/Cas9 knockout


title: breast cancer_MD36_S


title: lung alveolar organoid, Csnk2a1 knockout, plate3-2 well D05

description: Library name: 3-2_D05_CSNK2A1

value: Csnk2a1 CRISPR/Cas9 knockout


title: breast cancer_MD33_S


title: breast cancer_MD31_S

value: I


title: lung alveolar organoid, Egfl6 knockout, plate3-2 well D04

description: Library name: 3-2_D04_EGFL6

value: Egfl6 CRISPR/Cas9 knockout


title: breast cancer_MD30_S


title: breast cancer_MD27_S


title: lung alveolar organoid, Slc22a3 knockout, plate3-2 well D02

description: Library name: 3-2_D02_SLC22A3

value: Slc22a3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Erbb2 knockout, plate3-2 well D03

description: Library name: 3-2_D03_ERBB2

value: Erbb2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Cish knockout, plate3-2 well C11

description: Library name: 3-2_C11_CISH

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Cish CRISPR/Cas9 knockout


title: breast cancer_MD120_S


title: lung alveolar organoid, Map3k7 knockout, plate3-2 well C10

description: Library name: 3-2_C10_MAP3K7

value: Map3k7 CRISPR/Cas9 knockout


title: breast cancer_MD93_S

value: P

value: III


title: lung alveolar organoid, Tigit knockout, plate3-2 well C09

description: Library name: 3-2_C09_TIGIT


title: breast cancer_MD115_S

value: N


title: lung alveolar organoid, Ociad2 knockout, plate3-2 well C08

description: Library name: 3-2_C08_OCIAD2

value: Ociad2 CRISPR/Cas9 knockout


title: breast cancer_MD112_S

value: IIA

value: Tissue


title: lung alveolar organoid, Gnai2 knockout, plate3-2 well C07

description: Library name: 3-2_C07_GNAI2

value: Gnai2 CRISPR/Cas9 knockout


title: breast cancer_MD110_S

value: IIB

value: Surgical Tissue Sample


title: lung alveolar organoid, Adk knockout, plate3-2 well C06

description: Library name: 3-2_C06_ADK

value: Adk CRISPR/Cas9 knockout


title: breast cancer_MD105_S


title: breast cancer_MD108_S


title: lung alveolar organoid, Dram1 knockout, plate3-2 well C04

description: Library name: 3-2_C04_DRAM1

value: Dram1 CRISPR/Cas9 knockout


title: breast cancer_MD104_S


title: lung alveolar organoid, Csnk1a1 knockout, plate3-2 well C05

description: Library name: 3-2_C05_CSNK1A1

value: Csnk1a1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Egfr knockout, plate3-2 well C03

description: Library name: 3-2_C03_EGFR

value: Egfr CRISPR/Cas9 knockout


title: breast cancer_MD83_S


title: lung alveolar organoid, Itgb6 knockout, plate3-2 well C02

description: Library name: 3-2_C02_ITGB6

value: Itgb6 CRISPR/Cas9 knockout


title: breast cancer_MD82_S


title: lung alveolar organoid, Mapk3 knockout, plate3-2 well B11

description: Library name: 3-2_B11_MAPK3

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Mapk3 CRISPR/Cas9 knockout


title: breast cancer_MD69_S


title: breast cancer_MD67_S


title: lung alveolar organoid, Map3k5 knockout, plate3-2 well B10

description: Library name: 3-2_B10_MAP3K5

value: Map3k5 CRISPR/Cas9 knockout


title: breast cancer_MD66_S

value: P


title: lung alveolar organoid, Map2k2 knockout, plate3-2 well B09

description: Library name: 3-2_B09_MAP2K2

value: Map2k2 CRISPR/Cas9 knockout


title: breast cancer_MD50_S

value: N


title: lung alveolar organoid, Celsr1 knockout, plate3-2 well B07

description: Library name: 3-2_B07_CELSR1

value: Celsr1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Pi4k2b knockout, plate3-2 well B08

description: Library name: 3-2_B08_PI4K2B

value: Pi4k2b CRISPR/Cas9 knockout


title: breast cancer_MD49_S

value: Tissue


title: breast cancer_MD91_S


title: breast cancer_MD90_S


title: lung alveolar organoid, Tdtomato knockout, plate3-2 well B05

description: Library name: 3-2_B05_TDTOMATO

value: Tdtomato CRISPR/Cas9 knockout


title: lung alveolar organoid, Tgif1 knockout, plate3-2 well B06

description: Library name: 3-2_B06_TGIF1

value: Tgif1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate3-2 well B04

description: Library name: 3-2_B04_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_MD78_S

value: III

value: Surgical Tissue Sample


title: lung alveolar organoid, Cd81 knockout, plate3-2 well B03

description: Library name: 3-2_B03_CD81

value: Cd81 CRISPR/Cas9 knockout


title: breast cancer_MD71_S

value: IIB


title: lung alveolar organoid, Kidins220 knockout, plate3-2 well B02

description: Library name: 3-2_B02_KIDINS220

value: Kidins220 CRISPR/Cas9 knockout


title: breast cancer_MD97_S


title: lung alveolar organoid, Tigit knockout, plate3-1 well G11

description: Library name: 3-1_G11_TIGIT

value: lung mouse alveolar type 2 cells and primary human fibroblasts


title: breast cancer_MD74_S

value: IIA


title: breast cancer_945

value: Cytology

value: Needle Biopsy Sample


title: lung alveolar organoid, Tdtomato knockout, plate3-1 well G10

description: Library name: 3-1_G10_TDTOMATO


title: lung alveolar organoid, Map3k2 knockout, plate3-1 well G09

description: Library name: 3-1_G09_MAP3K2

value: Map3k2 CRISPR/Cas9 knockout


title: breast cancer_942

value: P

value: L

value: N


title: breast cancer_938


title: lung alveolar organoid, Map2k1 knockout, plate3-1 well G08

description: Library name: 3-1_G08_MAP2K1

value: Map2k1 CRISPR/Cas9 knockout


title: breast cancer_935


title: lung alveolar organoid, Atp6v0e knockout, plate3-1 well G07

description: Library name: 3-1_G07_ATP6V0E

value: Atp6v0e CRISPR/Cas9 knockout


title: lung alveolar organoid, Irf4 knockout, plate3-1 well G06

description: Library name: 3-1_G06_IRF4

value: Irf4 CRISPR/Cas9 knockout


title: breast cancer_934


title: lung alveolar organoid, Vangl2 knockout, plate3-1 well G05

description: Library name: 3-1_G05_VANGL2

value: Vangl2 CRISPR/Cas9 knockout


title: breast cancer_932


title: breast cancer_931

value: III


title: lung alveolar organoid, Soat1 knockout, plate3-1 well G04

description: Library name: 3-1_G04_SOAT1

value: Soat1 CRISPR/Cas9 knockout


title: breast cancer_929


title: lung alveolar organoid, Socs2 knockout, plate3-1 well G03

description: Library name: 3-1_G03_SOCS2

value: Socs2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Erbb3 knockout, plate3-1 well G02

description: Library name: 3-1_G02_ERBB3

value: Erbb3 CRISPR/Cas9 knockout


title: breast cancer_927


title: lung alveolar organoid, Bmp2 knockout, plate3-1 well F11

description: Library name: 3-1_F11_BMP2

value: Bmp2 CRISPR/Cas9 knockout


title: breast cancer_924


title: lung alveolar organoid, Map3k1 knockout, plate3-1 well F09

description: Library name: 3-1_F09_MAP3K1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Map3k1 CRISPR/Cas9 knockout


title: breast cancer_921

value: IIB

value: Cytology


title: breast cancer_925

value: Needle Biopsy Sample


title: lung alveolar organoid, Mapk1 knockout, plate3-1 well F10

description: Library name: 3-1_F10_MAPK1

value: Mapk1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tspan11 knockout, plate3-1 well F08

description: Library name: 3-1_F08_TSPAN11

value: Tspan11 CRISPR/Cas9 knockout


title: breast cancer_916

value: P

value: N


title: lung alveolar organoid, Areg knockout, plate3-1 well F07

description: Library name: 3-1_F07_AREG

value: Areg CRISPR/Cas9 knockout


title: breast cancer_913


title: lung alveolar organoid, Tinag knockout, plate3-1 well F06

description: Library name: 3-1_F06_TINAG

value: Tinag CRISPR/Cas9 knockout


title: breast cancer_912

value: IV


title: breast cancer_910

value: III


title: lung alveolar organoid, Vangl1 knockout, plate3-1 well F05

description: Library name: 3-1_F05_VANGL1

value: Vangl1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Slc39a8 knockout, plate3-1 well F04

description: Library name: 3-1_F04_SLC39A8

value: Slc39a8 CRISPR/Cas9 knockout


title: breast cancer_905

value: IIA


title: breast cancer_898

value: L


title: lung alveolar organoid, Erbb4 knockout, plate3-1 well F03

description: Library name: 3-1_F03_ERBB4

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Erbb4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate3-1 well F02

description: Library name: 3-1_F02_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_896

value: Cytology


title: lung alveolar organoid, Ccn2 knockout, plate3-1 well E11

description: Library name: 3-1_E11_CCN2

value: Ccn2 CRISPR/Cas9 knockout


title: breast cancer_894

value: Needle Biopsy Sample


title: lung alveolar organoid, Map4k4 knockout, plate3-1 well E10

description: Library name: 3-1_E10_MAP4K4

value: Map4k4 CRISPR/Cas9 knockout


title: breast cancer_893

value: P


title: lung alveolar organoid, Map2k4 knockout, plate3-1 well E09

description: Library name: 3-1_E09_MAP2K4

value: Map2k4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Antxr1 knockout, plate3-1 well E08

description: Library name: 3-1_E08_ANTXR1

value: Antxr1 CRISPR/Cas9 knockout


title: breast cancer_887

value: N


title: lung alveolar organoid, Gnai1 knockout, plate3-1 well E07

description: Library name: 3-1_E07_GNAI1

value: Gnai1 CRISPR/Cas9 knockout


title: breast cancer_886

value: IIB


title: breast cancer_892


title: lung alveolar organoid, Myo5c knockout, plate3-1 well E06

description: Library name: 3-1_E06_MYO5C

value: Myo5c CRISPR/Cas9 knockout


title: breast cancer_883


title: lung alveolar organoid, Csnk2a1 knockout, plate3-1 well E05

description: Library name: 3-1_E05_CSNK2A1

value: Csnk2a1 CRISPR/Cas9 knockout


title: breast cancer_880

value: IIA


title: lung alveolar organoid, Ctsh knockout, plate3-1 well E04

description: Library name: 3-1_E04_CTSH

value: Ctsh CRISPR/Cas9 knockout


title: breast cancer_878

value: III


title: lung alveolar organoid, Tigit knockout, plate3-1 well E03

description: Library name: 3-1_E03_TIGIT

value: lung mouse alveolar type 2 cells and primary human fibroblasts


title: breast cancer_872

value: I


title: breast cancer_871

value: L

value: Cytology


title: lung alveolar organoid, Tlr2 knockout, plate3-1 well E02

description: Library name: 3-1_E02_TLR2

value: Tlr2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Elf5 knockout, plate3-1 well D11

description: Library name: 3-1_D11_ELF5

value: Elf5 CRISPR/Cas9 knockout


title: breast cancer_868

value: P

value: Needle Biopsy Sample


title: lung alveolar organoid, Map4k3 knockout, plate3-1 well D10

description: Library name: 3-1_D10_MAP4K3

value: Map4k3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Map2k3 knockout, plate3-1 well D09

description: Library name: 3-1_D09_MAP2K3

value: Map2k3 CRISPR/Cas9 knockout


title: breast cancer_860

value: N


title: breast cancer_867


title: breast cancer_864

value: IV


title: lung alveolar organoid, Tigit knockout, plate3-1 well D07

description: Library name: 3-1_D07_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_857


title: lung alveolar organoid, Ank3 knockout, plate3-1 well D06

description: Library name: 3-1_D06_ANK3

value: Ank3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Elovl1 knockout, plate3-1 well D08

description: Library name: 3-1_D08_ELOVL1

value: Elovl1 CRISPR/Cas9 knockout


title: breast cancer_856

value: IIB


title: breast cancer_855

value: III


title: lung alveolar organoid, Egfl6 knockout, plate3-1 well D04

description: Library name: 3-1_D04_EGFL6

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Egfl6 CRISPR/Cas9 knockout


title: breast cancer_854

value: IIA


title: lung alveolar organoid, Erbb2 knockout, plate3-1 well D03

description: Library name: 3-1_D03_ERBB2

value: Erbb2 CRISPR/Cas9 knockout


title: breast cancer_845

value: Cytology


title: lung alveolar organoid, Slc22a3 knockout, plate3-1 well D02

description: Library name: 3-1_D02_SLC22A3

value: Slc22a3 CRISPR/Cas9 knockout


title: breast cancer_842

value: P


title: breast cancer_841

value: Needle Biopsy Sample


title: lung alveolar organoid, Cish knockout, plate3-1 well C11

description: Library name: 3-1_C11_CISH

value: Cish CRISPR/Cas9 knockout


title: breast cancer_839


title: lung alveolar organoid, Tigit knockout, plate3-1 well C09

description: Library name: 3-1_C09_TIGIT


title: breast cancer_838


title: lung alveolar organoid, Ociad2 knockout, plate3-1 well C08

description: Library name: 3-1_C08_OCIAD2

value: Ociad2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Map3k7 knockout, plate3-1 well C10

description: Library name: 3-1_C10_MAP3K7

value: Map3k7 CRISPR/Cas9 knockout


title: breast cancer_837

value: N


title: lung alveolar organoid, Csnk2a1 knockout, plate3-1 well D05

description: Library name: 3-1_D05_CSNK2A1

value: Csnk2a1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Gnai2 knockout, plate3-1 well C07

description: Library name: 3-1_C07_GNAI2

value: Gnai2 CRISPR/Cas9 knockout


title: breast cancer_835


title: breast cancer_833


title: breast cancer_832


title: lung alveolar organoid, Dram1 knockout, plate3-1 well C04

description: Library name: 3-1_C04_DRAM1

value: Dram1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Egfr knockout, plate3-1 well C03

description: Library name: 3-1_C03_EGFR

value: Egfr CRISPR/Cas9 knockout


title: breast cancer_828

value: III


title: breast cancer_831


title: lung alveolar organoid, Adk knockout, plate3-1 well C06

description: Library name: 3-1_C06_ADK

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Adk CRISPR/Cas9 knockout


title: lung alveolar organoid, Itgb6 knockout, plate3-1 well C02

description: Library name: 3-1_C02_ITGB6

value: Itgb6 CRISPR/Cas9 knockout


title: breast cancer_826

value: L

value: IIB


title: lung alveolar organoid, Mapk3 knockout, plate3-1 well B11

description: Library name: 3-1_B11_MAPK3

value: Mapk3 CRISPR/Cas9 knockout


title: breast cancer_825

value: P

value: IIA

value: Cytology


title: lung alveolar organoid, Map2k2 knockout, plate3-1 well B09

description: Library name: 3-1_B09_MAP2K2

value: Map2k2 CRISPR/Cas9 knockout


title: breast cancer_824

value: Needle Biopsy Sample


title: lung alveolar organoid, Map3k5 knockout, plate3-1 well B10

description: Library name: 3-1_B10_MAP3K5

value: Map3k5 CRISPR/Cas9 knockout


title: breast cancer_822

value: N


title: lung alveolar organoid, Csnk1a1 knockout, plate3-1 well C05

description: Library name: 3-1_C05_CSNK1A1

value: Csnk1a1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Pi4k2b knockout, plate3-1 well B08

description: Library name: 3-1_B08_PI4K2B

value: Pi4k2b CRISPR/Cas9 knockout


title: breast cancer_821


title: lung alveolar organoid, Tgif1 knockout, plate3-1 well B06

description: Library name: 3-1_B06_TGIF1

value: Tgif1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Celsr1 knockout, plate3-1 well B07

description: Library name: 3-1_B07_CELSR1

value: Celsr1 CRISPR/Cas9 knockout


title: breast cancer_817

value: III


title: lung alveolar organoid, Tdtomato knockout, plate3-1 well B05

description: Library name: 3-1_B05_TDTOMATO

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Tdtomato CRISPR/Cas9 knockout


title: breast cancer_815


title: breast cancer_816

value: I


title: breast cancer_814

value: L


title: lung alveolar organoid, Tigit knockout, plate3-1 well B04

description: Library name: 3-1_B04_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_813

value: P


title: lung alveolar organoid, Cd81 knockout, plate3-1 well B03

description: Library name: 3-1_B03_CD81

value: Cd81 CRISPR/Cas9 knockout


title: lung alveolar organoid, Kidins220 knockout, plate3-1 well B02

description: Library name: 3-1_B02_KIDINS220

value: Kidins220 CRISPR/Cas9 knockout


title: breast cancer_810

value: Cytology


title: lung alveolar organoid, Tigit knockout, plate2-4 well G11

description: Library name: 2-4_G11_TIGIT


title: breast cancer_806

value: IV

value: Needle Biopsy Sample


title: breast cancer_808

value: N

value: IIB


title: lung alveolar organoid, Tdtomato knockout, plate2-4 well G10

description: Library name: 2-4_G10_TDTOMATO


title: breast cancer_801


title: lung alveolar organoid, Dmbt1 knockout, plate2-4 well G09

description: Library name: 2-4_G09_DMBT1

value: Dmbt1 CRISPR/Cas9 knockout


title: breast cancer_795

value: IIA


title: lung alveolar organoid, Fzd4 knockout, plate2-4 well G07

description: Library name: 2-4_G07_FZD4

value: Fzd4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Myrf knockout, plate2-4 well G06

description: Library name: 2-4_G06_MYRF

value: Myrf CRISPR/Cas9 knockout


title: breast cancer_784

value: III


title: breast cancer_789


title: lung alveolar organoid, Fzd6 knockout, plate2-4 well G05

description: Library name: 2-4_G05_FZD6

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Fzd6 CRISPR/Cas9 knockout


title: breast cancer_782


title: lung alveolar organoid, Syt11 knockout, plate2-4 well G08

description: Library name: 2-4_G08_SYT11

value: Syt11 CRISPR/Cas9 knockout


title: breast cancer_776


title: lung alveolar organoid, Tert knockout, plate2-4 well G02

description: Library name: 2-4_G02_TERT

value: Tert CRISPR/Cas9 knockout


title: lung alveolar organoid, Bap1 knockout, plate2-4 well F11

description: Library name: 2-4_F11_BAP1

value: Bap1 CRISPR/Cas9 knockout


title: breast cancer_781

value: P


title: breast cancer_774


title: lung alveolar organoid, Fzd5 knockout, plate2-4 well G04

description: Library name: 2-4_G04_FZD5

value: Fzd5 CRISPR/Cas9 knockout


title: breast cancer_772

value: Cytology


title: lung alveolar organoid, Lrp2 knockout, plate2-4 well F10

description: Library name: 2-4_F10_LRP2

value: Lrp2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tln1 knockout, plate2-4 well F09

description: Library name: 2-4_F09_TLN1

value: Tln1 CRISPR/Cas9 knockout


title: breast cancer_767

value: N

value: Needle Biopsy Sample


title: breast cancer_770


title: lung alveolar organoid, Fzd1 knockout, plate2-4 well F07

description: Library name: 2-4_F07_FZD1

value: Fzd1 CRISPR/Cas9 knockout


title: breast cancer_765


title: lung alveolar organoid, Syt4 knockout, plate2-4 well F08

description: Library name: 2-4_F08_SYT4

value: Syt4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Fzd7 knockout, plate2-4 well F06

description: Library name: 2-4_F06_FZD7

value: Fzd7 CRISPR/Cas9 knockout


title: lung alveolar organoid, Epcam knockout, plate2-4 well F05

description: Library name: 2-4_F05_EPCAM

value: Epcam CRISPR/Cas9 knockout


title: breast cancer_764

value: IIB


title: breast cancer_755

value: III


title: breast cancer_753


title: lung alveolar organoid, Mtus1 knockout, plate2-4 well F04

description: Library name: 2-4_F04_MTUS1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Mtus1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Dsp knockout, plate2-4 well F03

description: Library name: 2-4_F03_DSP

value: Dsp CRISPR/Cas9 knockout


title: breast cancer_748

value: IIA


title: lung alveolar organoid, Tigit knockout, plate2-4 well F02

description: Library name: 2-4_F02_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_746

value: P


title: breast cancer_744

value: Cytology


title: lung alveolar organoid, Csf3r knockout, plate2-4 well E11

description: Library name: 2-4_E11_CSF3R

value: Csf3r CRISPR/Cas9 knockout


title: lung alveolar organoid, Ros1 knockout, plate2-4 well E10

description: Library name: 2-4_E10_ROS1

value: Ros1 CRISPR/Cas9 knockout


title: breast cancer_734

value: N


title: lung alveolar organoid, Sh2b1 knockout, plate2-4 well E09

description: Library name: 2-4_E09_SH2B1

value: Sh2b1 CRISPR/Cas9 knockout


title: breast cancer_733

value: Needle Biopsy Sample


title: lung alveolar organoid, Chrna3 knockout, plate2-4 well E08

description: Library name: 2-4_E08_CHRNA3

value: Chrna3 CRISPR/Cas9 knockout


title: breast cancer_728


title: breast cancer_725


title: breast cancer_726

value: IV


title: breast cancer_723


title: lung alveolar organoid, Cxadr knockout, plate2-4 well E05

description: Library name: 2-4_E05_CXADR

value: Cxadr CRISPR/Cas9 knockout


title: lung alveolar organoid, Lrp6 knockout, plate2-4 well E07

description: Library name: 2-4_E07_LRP6

value: Lrp6 CRISPR/Cas9 knockout


title: lung alveolar organoid, Fgfr2 knockout, plate2-4 well E06

description: Library name: 2-4_E06_FGFR2

value: Fgfr2 CRISPR/Cas9 knockout


title: breast cancer_720


title: lung alveolar organoid, Tigit knockout, plate2-4 well E03

description: Library name: 2-4_E03_TIGIT

value: lung mouse alveolar type 2 cells and primary human fibroblasts


title: lung alveolar organoid, Tollip knockout, plate2-4 well E04

description: Library name: 2-4_E04_TOLLIP

value: Tollip CRISPR/Cas9 knockout


title: breast cancer_717


title: breast cancer_714

value: IIB


title: lung alveolar organoid, Mecom knockout, plate2-4 well E02

description: Library name: 2-4_E02_MECOM

value: Mecom CRISPR/Cas9 knockout


title: lung alveolar organoid, Etv5 knockout, plate2-4 well D11

description: Library name: 2-4_D11_ETV5

value: Etv5 CRISPR/Cas9 knockout


title: breast cancer_710

value: P

value: IIA


title: lung alveolar organoid, Hif1a knockout, plate2-4 well D10

description: Library name: 2-4_D10_HIF1A

value: Hif1a CRISPR/Cas9 knockout


title: breast cancer_706

value: III

value: Cytology


title: lung alveolar organoid, Wnt9b knockout, plate2-4 well D08

description: Library name: 2-4_D08_WNT9B

value: Wnt9b CRISPR/Cas9 knockout


title: breast cancer_702

value: N

value: Needle Biopsy Sample


title: lung alveolar organoid, Spns1 knockout, plate2-4 well D09

description: Library name: 2-4_D09_SPNS1

value: Spns1 CRISPR/Cas9 knockout


title: breast cancer_705


title: lung alveolar organoid, Tigit knockout, plate2-4 well D07

description: Library name: 2-4_D07_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: lung alveolar organoid, Liph knockout, plate2-4 well D06

description: Library name: 2-4_D06_LIPH

value: Liph CRISPR/Cas9 knockout


title: breast cancer_700


title: breast cancer_697

value: IV


title: lung alveolar organoid, Slc45a4 knockout, plate2-4 well D05

description: Library name: 2-4_D05_SLC45A4

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Slc45a4 CRISPR/Cas9 knockout


title: breast cancer_695

value: IIB


title: lung alveolar organoid, Sdc1 knockout, plate2-4 well D04

description: Library name: 2-4_D04_SDC1

value: Sdc1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Gpr37 knockout, plate2-4 well D03

description: Library name: 2-4_D03_GPR37

value: Gpr37 CRISPR/Cas9 knockout


title: breast cancer_691

value: P


title: breast cancer_693


title: lung alveolar organoid, Capn1 knockout, plate2-4 well D02

description: Library name: 2-4_D02_CAPN1

value: Capn1 CRISPR/Cas9 knockout


title: breast cancer_690


title: lung alveolar organoid, Irx1 knockout, plate2-4 well C11

description: Library name: 2-4_C11_IRX1

value: Irx1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Hlf knockout, plate2-4 well C10

description: Library name: 2-4_C10_HLF

value: Hlf CRISPR/Cas9 knockout


title: breast cancer_682

value: IIA

value: Cytology


title: breast cancer_685

value: N


title: lung alveolar organoid, Tigit knockout, plate2-4 well C09

description: Library name: 2-4_C09_TIGIT


title: breast cancer_671

value: Needle Biopsy Sample


title: breast cancer_680

value: III


title: breast cancer_669


title: breast cancer_668


title: lung alveolar organoid, Megf6 knockout, plate2-4 well C05

description: Library name: 2-4_C05_MEGF6

value: Megf6 CRISPR/Cas9 knockout


title: lung alveolar organoid, Snx30 knockout, plate2-4 well C06

description: Library name: 2-4_C06_SNX30

value: Snx30 CRISPR/Cas9 knockout


title: breast cancer_666


title: lung alveolar organoid, Patj knockout, plate2-4 well C04

description: Library name: 2-4_C04_PATJ

value: Patj CRISPR/Cas9 knockout


title: lung alveolar organoid, Chat knockout, plate2-4 well C07

description: Library name: 2-4_C07_CHAT

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Chat CRISPR/Cas9 knockout


title: breast cancer_663


title: lung alveolar organoid, Atp11a knockout, plate2-4 well C03

description: Library name: 2-4_C03_ATP11A

value: Atp11a CRISPR/Cas9 knockout


title: lung alveolar organoid, Wnt7b knockout, plate2-4 well C08

description: Library name: 2-4_C08_WNT7B

value: Wnt7b CRISPR/Cas9 knockout


title: breast cancer_662

value: IIB


title: lung alveolar organoid, Nav2 knockout, plate2-4 well C02

description: Library name: 2-4_C02_NAV2

value: Nav2 CRISPR/Cas9 knockout


title: breast cancer_654

value: P


title: lung alveolar organoid, Atp6v1c2 knockout, plate2-4 well B11

description: Library name: 2-4_B11_ATP6V1C2

value: Atp6v1c2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Il4ra knockout, plate2-4 well B10

description: Library name: 2-4_B10_IL4RA

value: Il4ra CRISPR/Cas9 knockout


title: breast cancer_660

value: IIA


title: breast cancer_652

value: Cytology


title: breast cancer_651

value: N


title: lung alveolar organoid, Trib3 knockout, plate2-4 well B09

description: Library name: 2-4_B09_TRIB3

value: Trib3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Marcks knockout, plate2-4 well B08

description: Library name: 2-4_B08_MARCKS

value: Marcks CRISPR/Cas9 knockout


title: breast cancer_650

value: III

value: Needle Biopsy Sample


title: lung alveolar organoid, Chrna5 knockout, plate2-4 well B07

description: Library name: 2-4_B07_CHRNA5

value: Chrna5 CRISPR/Cas9 knockout


title: breast cancer_646

value: L


title: breast cancer_645


title: breast cancer_644


title: lung alveolar organoid, Tdtomato knockout, plate2-4 well B05

description: Library name: 2-4_B05_TDTOMATO

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Tdtomato CRISPR/Cas9 knockout


title: breast cancer_643


title: lung alveolar organoid, Lnx2 knockout, plate2-4 well B06

description: Library name: 2-4_B06_LNX2

value: Lnx2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate2-4 well B04

description: Library name: 2-4_B04_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: lung alveolar organoid, Acoxl knockout, plate2-4 well B03

description: Library name: 2-4_B03_ACOXL

value: Acoxl CRISPR/Cas9 knockout


title: breast cancer_642

value: P


title: lung alveolar organoid, Tigit knockout, plate2-3 well G11

description: Library name: 2-3_G11_TIGIT


title: breast cancer_640

value: IV


title: breast cancer_637

value: IIB


title: lung alveolar organoid, Tdtomato knockout, plate2-3 well G10

description: Library name: 2-3_G10_TDTOMATO


title: breast cancer_636

value: IIA


title: lung alveolar organoid, Dmbt1 knockout, plate2-3 well G09

description: Library name: 2-3_G09_DMBT1

value: Dmbt1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Syt11 knockout, plate2-3 well G08

description: Library name: 2-3_G08_SYT11

value: Syt11 CRISPR/Cas9 knockout


title: breast cancer_632

value: N

value: Cytology


title: lung alveolar organoid, Fzd4 knockout, plate2-3 well G07

description: Library name: 2-3_G07_FZD4

value: Fzd4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Myrf knockout, plate2-3 well G06

description: Library name: 2-3_G06_MYRF

value: Myrf CRISPR/Cas9 knockout


title: breast cancer_629

value: Needle Biopsy Sample


title: lung alveolar organoid, Fzd6 knockout, plate2-3 well G05

description: Library name: 2-3_G05_FZD6

value: Fzd6 CRISPR/Cas9 knockout


title: breast cancer_631

value: III


title: breast cancer_618

value: L


title: lung alveolar organoid, Lrp5 knockout, plate2-3 well G03

description: Library name: 2-3_G03_LRP5

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Lrp5 CRISPR/Cas9 knockout


title: breast cancer_610


title: lung alveolar organoid, Tert knockout, plate2-3 well G02

description: Library name: 2-3_G02_TERT

value: Tert CRISPR/Cas9 knockout


title: lung alveolar organoid, Bap1 knockout, plate2-3 well F11

description: Library name: 2-3_F11_BAP1

value: Bap1 CRISPR/Cas9 knockout


title: breast cancer_607

value: P


title: lung alveolar organoid, Lrp2 knockout, plate2-3 well F10

description: Library name: 2-3_F10_LRP2

value: Lrp2 CRISPR/Cas9 knockout


title: breast cancer_606

value: IIA


title: breast cancer_604


title: lung alveolar organoid, Tln1 knockout, plate2-3 well F09

description: Library name: 2-3_F09_TLN1

value: Tln1 CRISPR/Cas9 knockout


title: breast cancer_599


title: breast cancer_598


title: lung alveolar organoid, Fzd1 knockout, plate2-3 well F07

description: Library name: 2-3_F07_FZD1

value: Fzd1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Syt4 knockout, plate2-3 well F08

description: Library name: 2-3_F08_SYT4

value: Syt4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Fzd7 knockout, plate2-3 well F06

description: Library name: 2-3_F06_FZD7

value: Fzd7 CRISPR/Cas9 knockout


title: breast cancer_597

value: N

value: Cytology


title: breast cancer_581

value: Needle Biopsy Sample


title: lung alveolar organoid, Epcam knockout, plate2-3 well F05

description: Library name: 2-3_F05_EPCAM

value: Epcam CRISPR/Cas9 knockout


title: breast cancer_580

value: III


title: breast cancer_578


title: breast cancer_577

value: IIB


title: lung alveolar organoid, Dsp knockout, plate2-3 well F03

description: Library name: 2-3_F03_DSP

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Dsp CRISPR/Cas9 knockout


title: lung alveolar organoid, Mtus1 knockout, plate2-3 well F04

description: Library name: 2-3_F04_MTUS1

value: Mtus1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate2-3 well F02

description: Library name: 2-3_F02_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_575

value: P

value: L


title: breast cancer_566


title: lung alveolar organoid, Ros1 knockout, plate2-3 well E10

description: Library name: 2-3_E10_ROS1

value: Ros1 CRISPR/Cas9 knockout


title: breast cancer_569


title: breast cancer_565


title: lung alveolar organoid, Sh2b1 knockout, plate2-3 well E09

description: Library name: 2-3_E09_SH2B1

value: Sh2b1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Csf3r knockout, plate2-3 well E11

description: Library name: 2-3_E11_CSF3R

value: Csf3r CRISPR/Cas9 knockout


title: lung alveolar organoid, Chrna3 knockout, plate2-3 well E08

description: Library name: 2-3_E08_CHRNA3

value: Chrna3 CRISPR/Cas9 knockout


title: breast cancer_559


title: breast cancer_556

value: IIA


title: lung alveolar organoid, Fgfr2 knockout, plate2-3 well E06

description: Library name: 2-3_E06_FGFR2

value: Fgfr2 CRISPR/Cas9 knockout


title: breast cancer_551

value: N

value: Cytology


title: lung alveolar organoid, Cxadr knockout, plate2-3 well E05

description: Library name: 2-3_E05_CXADR

value: Cxadr CRISPR/Cas9 knockout


title: breast cancer_549

value: Needle Biopsy Sample


title: lung alveolar organoid, Lrp6 knockout, plate2-3 well E07

description: Library name: 2-3_E07_LRP6

value: Lrp6 CRISPR/Cas9 knockout


title: breast cancer_540

value: IIB


title: lung alveolar organoid, Tollip knockout, plate2-3 well E04

description: Library name: 2-3_E04_TOLLIP

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Tollip CRISPR/Cas9 knockout


title: breast cancer_539

value: III


title: lung alveolar organoid, Tigit knockout, plate2-3 well E03

description: Library name: 2-3_E03_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_536

value: P


title: lung alveolar organoid, Mecom knockout, plate2-3 well E02

description: Library name: 2-3_E02_MECOM

value: Mecom CRISPR/Cas9 knockout


title: lung alveolar organoid, Etv5 knockout, plate2-3 well D11

description: Library name: 2-3_D11_ETV5

value: Etv5 CRISPR/Cas9 knockout


title: breast cancer_528


title: breast cancer_527


title: lung alveolar organoid, Hif1a knockout, plate2-3 well D10

description: Library name: 2-3_D10_HIF1A

value: Hif1a CRISPR/Cas9 knockout


title: lung alveolar organoid, Wnt9b knockout, plate2-3 well D08

description: Library name: 2-3_D08_WNT9B

value: Wnt9b CRISPR/Cas9 knockout


title: breast cancer_510

value: L

value: IV


title: breast cancer_508

value: N


title: lung alveolar organoid, Spns1 knockout, plate2-3 well D09

description: Library name: 2-3_D09_SPNS1

value: Spns1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate2-3 well D07

description: Library name: 2-3_D07_TIGIT


title: breast cancer_507

value: IIA

value: Cytology


title: lung alveolar organoid, Slc45a4 knockout, plate2-3 well D05

description: Library name: 2-3_D05_SLC45A4

value: Slc45a4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Liph knockout, plate2-3 well D06

description: Library name: 2-3_D06_LIPH

value: Liph CRISPR/Cas9 knockout


title: breast cancer_504

value: Needle Biopsy Sample


title: lung alveolar organoid, Sdc1 knockout, plate2-3 well D04

description: Library name: 2-3_D04_SDC1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Sdc1 CRISPR/Cas9 knockout


title: breast cancer_505

value: I


title: breast cancer_496

value: P

value: IIB


title: lung alveolar organoid, Gpr37 knockout, plate2-3 well D03

description: Library name: 2-3_D03_GPR37

value: Gpr37 CRISPR/Cas9 knockout


title: breast cancer_486


title: breast cancer_477


title: lung alveolar organoid, Hlf knockout, plate2-3 well C10

description: Library name: 2-3_C10_HLF

value: Hlf CRISPR/Cas9 knockout


title: lung alveolar organoid, Capn1 knockout, plate2-3 well D02

description: Library name: 2-3_D02_CAPN1

value: Capn1 CRISPR/Cas9 knockout


title: breast cancer_480


title: lung alveolar organoid, Wnt7b knockout, plate2-3 well C08

description: Library name: 2-3_C08_WNT7B

value: Wnt7b CRISPR/Cas9 knockout


title: breast cancer_472

value: III


title: breast cancer_470

value: N


title: breast cancer_476


title: breast cancer_466


title: lung alveolar organoid, Snx30 knockout, plate2-3 well C06

description: Library name: 2-3_C06_SNX30

value: Snx30 CRISPR/Cas9 knockout


title: lung alveolar organoid, Chat knockout, plate2-3 well C07

description: Library name: 2-3_C07_CHAT

value: Chat CRISPR/Cas9 knockout


title: lung alveolar organoid, Megf6 knockout, plate2-3 well C05

description: Library name: 2-3_C05_MEGF6

value: Megf6 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate2-3 well C09

description: Library name: 2-3_C09_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_461

value: IIA

value: Cytology


title: breast cancer_453

value: IV

value: Needle Biopsy Sample


title: lung alveolar organoid, Nav2 knockout, plate2-3 well C02

description: Library name: 2-3_C02_NAV2

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Nav2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Atp11a knockout, plate2-3 well C03

description: Library name: 2-3_C03_ATP11A

value: Atp11a CRISPR/Cas9 knockout


title: lung alveolar organoid, Patj knockout, plate2-3 well C04

description: Library name: 2-3_C04_PATJ

value: Patj CRISPR/Cas9 knockout


title: breast cancer_456

value: P


title: breast cancer_452

value: L

value: IIB


title: lung alveolar organoid, Atp6v1c2 knockout, plate2-3 well B11

description: Library name: 2-3_B11_ATP6V1C2

value: Atp6v1c2 CRISPR/Cas9 knockout


title: breast cancer_444

value: N


title: breast cancer_440


title: breast cancer_438

value: III


title: lung alveolar organoid, Trib3 knockout, plate2-3 well B09

description: Library name: 2-3_B09_TRIB3

value: Trib3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Il4ra knockout, plate2-3 well B10

description: Library name: 2-3_B10_IL4RA

value: Il4ra CRISPR/Cas9 knockout


title: lung alveolar organoid, Marcks knockout, plate2-3 well B08

description: Library name: 2-3_B08_MARCKS

value: Marcks CRISPR/Cas9 knockout


title: lung alveolar organoid, Chrna5 knockout, plate2-3 well B07

description: Library name: 2-3_B07_CHRNA5

value: Chrna5 CRISPR/Cas9 knockout


title: breast cancer_435

value: Cytology


title: breast cancer_433

value: IIA


title: lung alveolar organoid, Lnx2 knockout, plate2-3 well B06

description: Library name: 2-3_B06_LNX2

value: Lnx2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tdtomato knockout, plate2-3 well B05

description: Library name: 2-3_B05_TDTOMATO

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Tdtomato CRISPR/Cas9 knockout


title: breast cancer_431

value: Needle Biopsy Sample


title: breast cancer_424

value: IV


title: breast cancer_423

value: P


title: lung alveolar organoid, Ivd knockout, plate2-3 well B02

description: Library name: 2-3_B02_IVD

value: Ivd CRISPR/Cas9 knockout


title: lung alveolar organoid, Tdtomato knockout, plate2-2 well G10

description: Library name: 2-2_G10_TDTOMATO


title: lung alveolar organoid, Tigit knockout, plate2-3 well B04

description: Library name: 2-3_B04_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: lung alveolar organoid, Dmbt1 knockout, plate2-2 well G09

description: Library name: 2-2_G09_DMBT1

value: Dmbt1 CRISPR/Cas9 knockout


title: breast cancer_417

value: N


title: breast cancer_420


title: lung alveolar organoid, Syt11 knockout, plate2-2 well G08

description: Library name: 2-2_G08_SYT11

value: Syt11 CRISPR/Cas9 knockout


title: breast cancer_396

value: IIB


title: breast cancer_400


title: lung alveolar organoid, Fzd4 knockout, plate2-2 well G07

description: Library name: 2-2_G07_FZD4

value: Fzd4 CRISPR/Cas9 knockout


title: breast cancer_437

value: L


title: lung alveolar organoid, Myrf knockout, plate2-2 well G06

description: Library name: 2-2_G06_MYRF

value: Myrf CRISPR/Cas9 knockout


title: breast cancer_380

value: III

value: Cytology


title: breast cancer_379


title: breast cancer_378


title: lung alveolar organoid, Fzd6 knockout, plate2-2 well G05

description: Library name: 2-2_G05_FZD6

value: Fzd6 CRISPR/Cas9 knockout


title: lung alveolar organoid, Lrp5 knockout, plate2-2 well G03

description: Library name: 2-2_G03_LRP5

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Lrp5 CRISPR/Cas9 knockout


title: lung alveolar organoid, Fzd5 knockout, plate2-2 well G04

description: Library name: 2-2_G04_FZD5

value: Fzd5 CRISPR/Cas9 knockout


title: breast cancer_366

value: Needle Biopsy Sample


title: breast cancer_365

value: P


title: breast cancer_364


title: lung alveolar organoid, Lrp2 knockout, plate2-2 well F10

description: Library name: 2-2_F10_LRP2

value: Lrp2 CRISPR/Cas9 knockout


title: breast cancer_363


title: lung alveolar organoid, Bap1 knockout, plate2-2 well F11

description: Library name: 2-2_F11_BAP1

value: Bap1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tln1 knockout, plate2-2 well F09

description: Library name: 2-2_F09_TLN1

value: Tln1 CRISPR/Cas9 knockout


title: breast cancer_360

value: N


title: lung alveolar organoid, Syt4 knockout, plate2-2 well F08

description: Library name: 2-2_F08_SYT4

value: Syt4 CRISPR/Cas9 knockout


title: breast cancer_355

value: IIB


title: lung alveolar organoid, Fzd1 knockout, plate2-2 well F07

description: Library name: 2-2_F07_FZD1

value: Fzd1 CRISPR/Cas9 knockout


title: breast cancer_352


title: lung alveolar organoid, Epcam knockout, plate2-2 well F05

description: Library name: 2-2_F05_EPCAM

value: Epcam CRISPR/Cas9 knockout


title: lung alveolar organoid, Fzd7 knockout, plate2-2 well F06

description: Library name: 2-2_F06_FZD7

value: Fzd7 CRISPR/Cas9 knockout


title: breast cancer_349

value: IIA


title: breast cancer_342

value: Cytology


title: lung alveolar organoid, Tert knockout, plate2-2 well G02

description: Library name: 2-2_G02_TERT

value: Tert CRISPR/Cas9 knockout


title: breast cancer_340

value: L

value: III


title: breast cancer_338


title: lung alveolar organoid, Mtus1 knockout, plate2-2 well F04

description: Library name: 2-2_F04_MTUS1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Mtus1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate2-2 well F02

description: Library name: 2-2_F02_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: lung alveolar organoid, Dsp knockout, plate2-2 well F03

description: Library name: 2-2_F03_DSP

value: Dsp CRISPR/Cas9 knockout


title: breast cancer_337

value: P

value: Needle Biopsy Sample


title: breast cancer_335

value: N


title: lung alveolar organoid, Csf3r knockout, plate2-2 well E11

description: Library name: 2-2_E11_CSF3R

value: Csf3r CRISPR/Cas9 knockout


title: breast cancer_332


title: lung alveolar organoid, Sh2b1 knockout, plate2-2 well E09

description: Library name: 2-2_E09_SH2B1

value: Sh2b1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Ros1 knockout, plate2-2 well E10

description: Library name: 2-2_E10_ROS1

value: Ros1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Chrna3 knockout, plate2-2 well E08

description: Library name: 2-2_E08_CHRNA3

value: Chrna3 CRISPR/Cas9 knockout


title: breast cancer_327


title: breast cancer_325

value: IV


title: lung alveolar organoid, Lrp6 knockout, plate2-2 well E07

description: Library name: 2-2_E07_LRP6

value: Lrp6 CRISPR/Cas9 knockout


title: breast cancer_319

value: IIA

value: Cytology


title: lung alveolar organoid, Fgfr2 knockout, plate2-2 well E06

description: Library name: 2-2_E06_FGFR2

value: Fgfr2 CRISPR/Cas9 knockout


title: breast cancer_323

value: IIB


title: lung alveolar organoid, Cxadr knockout, plate2-2 well E05

description: Library name: 2-2_E05_CXADR

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Cxadr CRISPR/Cas9 knockout


title: breast cancer_313


title: lung alveolar organoid, Tollip knockout, plate2-2 well E04

description: Library name: 2-2_E04_TOLLIP

value: Tollip CRISPR/Cas9 knockout


title: breast cancer_305


title: breast cancer_312

value: L

value: III


title: lung alveolar organoid, Tigit knockout, plate2-2 well E03

description: Library name: 2-2_E03_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_300

value: P

value: N

value: Needle Biopsy Sample


title: lung alveolar organoid, Mecom knockout, plate2-2 well E02

description: Library name: 2-2_E02_MECOM

value: Mecom CRISPR/Cas9 knockout


title: lung alveolar organoid, Etv5 knockout, plate2-2 well D11

description: Library name: 2-2_D11_ETV5

value: Etv5 CRISPR/Cas9 knockout


title: breast cancer_288


title: breast cancer_290


title: lung alveolar organoid, Hif1a knockout, plate2-2 well D10

description: Library name: 2-2_D10_HIF1A

value: Hif1a CRISPR/Cas9 knockout


title: breast cancer_285


title: lung alveolar organoid, Spns1 knockout, plate2-2 well D09

description: Library name: 2-2_D09_SPNS1

value: Spns1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Wnt9b knockout, plate2-2 well D08

description: Library name: 2-2_D08_WNT9B

value: Wnt9b CRISPR/Cas9 knockout


title: breast cancer_283

value: Cytology


title: breast cancer_281

value: IIA


title: lung alveolar organoid, Tigit knockout, plate2-2 well D07

description: Library name: 2-2_D07_TIGIT


title: breast cancer_269


title: lung alveolar organoid, Liph knockout, plate2-2 well D06

description: Library name: 2-2_D06_LIPH

value: Liph CRISPR/Cas9 knockout


title: lung alveolar organoid, Slc45a4 knockout, plate2-2 well D05

description: Library name: 2-2_D05_SLC45A4

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Slc45a4 CRISPR/Cas9 knockout


title: breast cancer_263

value: IIB


title: breast cancer_268


title: lung alveolar organoid, Sdc1 knockout, plate2-2 well D04

description: Library name: 2-2_D04_SDC1

value: Sdc1 CRISPR/Cas9 knockout


title: breast cancer_247


title: lung alveolar organoid, Gpr37 knockout, plate2-2 well D03

description: Library name: 2-2_D03_GPR37

value: Gpr37 CRISPR/Cas9 knockout


title: lung alveolar organoid, Capn1 knockout, plate2-2 well D02

description: Library name: 2-2_D02_CAPN1

value: Capn1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Irx1 knockout, plate2-2 well C11

description: Library name: 2-2_C11_IRX1

value: Irx1 CRISPR/Cas9 knockout


title: breast cancer_240

value: P

value: N


title: breast cancer_225

value: Needle Biopsy Sample


title: lung alveolar organoid, Hlf knockout, plate2-2 well C10

description: Library name: 2-2_C10_HLF

value: Hlf CRISPR/Cas9 knockout


title: breast cancer_223


title: breast cancer_208


title: lung alveolar organoid, Tigit knockout, plate2-2 well C09

description: Library name: 2-2_C09_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_203

value: III


title: breast cancer_195


title: lung alveolar organoid, Chat knockout, plate2-2 well C07

description: Library name: 2-2_C07_CHAT

value: Chat CRISPR/Cas9 knockout


title: lung alveolar organoid, Wnt7b knockout, plate2-2 well C08

description: Library name: 2-2_C08_WNT7B

value: Wnt7b CRISPR/Cas9 knockout


title: lung alveolar organoid, Snx30 knockout, plate2-2 well C06

description: Library name: 2-2_C06_SNX30

value: Snx30 CRISPR/Cas9 knockout


title: breast cancer_144

value: Cytology


title: breast cancer_171


title: lung alveolar organoid, Megf6 knockout, plate2-2 well C05

description: Library name: 2-2_C05_MEGF6

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Megf6 CRISPR/Cas9 knockout


title: lung alveolar organoid, Patj knockout, plate2-2 well C04

description: Library name: 2-2_C04_PATJ

value: Patj CRISPR/Cas9 knockout


title: breast cancer_SM512

value: IIA

value: Surgical Tissue Sample


title: lung alveolar organoid, Atp11a knockout, plate2-2 well C03

description: Library name: 2-2_C03_ATP11A

value: Atp11a CRISPR/Cas9 knockout


title: breast cancer_142

value: IV


title: breast cancer_SM511

value: P

value: L

value: Tissue


title: lung alveolar organoid, Atp6v1c2 knockout, plate2-2 well B11

description: Library name: 2-2_B11_ATP6V1C2

value: Atp6v1c2 CRISPR/Cas9 knockout


title: breast cancer_SM510

value: N


title: breast cancer_SM509

value: Needle Biopsy Sample


title: lung alveolar organoid, Il4ra knockout, plate2-2 well B10

description: Library name: 2-2_B10_IL4RA

value: Il4ra CRISPR/Cas9 knockout


title: breast cancer_SM508

value: IIB


title: lung alveolar organoid, Trib3 knockout, plate2-2 well B09

description: Library name: 2-2_B09_TRIB3

value: Trib3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Nav2 knockout, plate2-2 well C02

description: Library name: 2-2_C02_NAV2

value: Nav2 CRISPR/Cas9 knockout


title: breast cancer_SM502

value: Cytology


title: lung alveolar organoid, Marcks knockout, plate2-2 well B08

description: Library name: 2-2_B08_MARCKS

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Marcks CRISPR/Cas9 knockout


title: lung alveolar organoid, Chrna5 knockout, plate2-2 well B07

description: Library name: 2-2_B07_CHRNA5

value: Chrna5 CRISPR/Cas9 knockout


title: lung alveolar organoid, Lnx2 knockout, plate2-2 well B06

description: Library name: 2-2_B06_LNX2

value: Lnx2 CRISPR/Cas9 knockout


title: breast cancer_SM501

value: I

value: Surgical Tissue Sample


title: breast cancer_SM500

value: P


title: lung alveolar organoid, Tdtomato knockout, plate2-2 well B05

description: Library name: 2-2_B05_TDTOMATO

value: Tdtomato CRISPR/Cas9 knockout


title: breast cancer_SM498

value: IIA

value: Tissue


title: breast cancer_SM497

value: N


title: lung alveolar organoid, Tigit knockout, plate2-2 well B04

description: Library name: 2-2_B04_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM496

value: IV

value: Needle Biopsy Sample


title: lung alveolar organoid, Acoxl knockout, plate2-2 well B03

description: Library name: 2-2_B03_ACOXL

value: Acoxl CRISPR/Cas9 knockout


title: lung alveolar organoid, Ivd knockout, plate2-2 well B02

description: Library name: 2-2_B02_IVD

value: Ivd CRISPR/Cas9 knockout


title: breast cancer_SM495


title: breast cancer_SM494


title: lung alveolar organoid, Tigit knockout, plate1-4 well G11

description: Library name: 1-4_G11_TIGIT


title: lung alveolar organoid, Tdtomato knockout, plate1-4 well G10

description: Library name: 1-4_G10_TDTOMATO


title: breast cancer_SM493


title: lung alveolar organoid, Becn1 knockout, plate1-4 well G09

description: Library name: 1-4_G09_BECLN1

value: Becn1 CRISPR/Cas9 knockout


title: breast cancer_SM491


title: breast cancer_SM490

value: IIB

value: Cytology


title: breast cancer_ER 227

value: Recurrent Tumor Biopsy


title: lung alveolar organoid, Ern1 knockout, plate1-4 well G08

description: Library name: 1-4_G08_ERN1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Ern1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Nr1d2 knockout, plate1-4 well G07

description: Library name: 1-4_G07_NR1D2

value: Nr1d2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Hhip knockout, plate1-4 well G06

description: Library name: 1-4_G06_HHIP

value: Hhip CRISPR/Cas9 knockout


title: breast cancer_SM489

value: P

value: I

value: Surgical Tissue Sample


title: breast cancer_SM488

value: N

value: IIA

value: Tissue


title: breast cancer_SM487


title: breast cancer_SM486

value: Needle Biopsy Sample


title: lung alveolar organoid, Cacna2d3 knockout, plate1-4 well G04

description: Library name: 1-4_G04_CACNA2D3

value: Cacna2d3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Chrm3 knockout, plate1-4 well G05

description: Library name: 1-4_G05_CHRM3

value: Chrm3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Serpina1a knockout, plate1-4 well G03

description: Library name: 1-4_G03_SERPINA1A

value: Serpina1a CRISPR/Cas9 knockout


title: lung alveolar organoid, Pid1 knockout, plate1-4 well G02

description: Library name: 1-4_G02_PID1

value: Pid1 CRISPR/Cas9 knockout


title: breast cancer_SM483


title: breast cancer_SM482

value: IIB


title: lung alveolar organoid, Irf4 knockout, plate3-4 well G06

description: Library name: 3-4_G06_IRF4

value: Irf4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Rad21 knockout, plate1-4 well F11

description: Library name: 1-4_F11_RAD21

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Rad21 CRISPR/Cas9 knockout


title: breast cancer_SM481


title: lung alveolar organoid, Xbp1 knockout, plate1-4 well F10

description: Library name: 1-4_F10_XBP1

value: Xbp1 CRISPR/Cas9 knockout


title: breast cancer_SM480


title: lung alveolar organoid, Atg16l1 knockout, plate1-4 well F09

description: Library name: 1-4_F09_ATG16L1

value: Atg16l1 CRISPR/Cas9 knockout


title: breast cancer_SM479

value: P


title: lung alveolar organoid, Eif2b1 knockout, plate1-4 well F08

description: Library name: 1-4_F08_EIF2B1

value: Eif2b1 CRISPR/Cas9 knockout


title: breast cancer_SM478

value: Surgical Tissue Sample


title: lung alveolar organoid, Fam13a knockout, plate1-4 well F06

description: Library name: 1-4_F06_FAM13A

value: Fam13a CRISPR/Cas9 knockout


title: lung alveolar organoid, Nr1d1 knockout, plate1-4 well F07

description: Library name: 1-4_F07_NR1D1

value: Nr1d1 CRISPR/Cas9 knockout


title: breast cancer_SM472

value: N

value: IIA

value: Tissue


title: breast cancer_SM473

value: Needle Biopsy Sample


title: lung alveolar organoid, Terf1 knockout, plate1-4 well F05

description: Library name: 1-4_F05_TERF1

value: Terf1 CRISPR/Cas9 knockout


title: breast cancer_SM471


title: lung alveolar organoid, Ager knockout, plate1-4 well F04

description: Library name: 1-4_F04_AGER

value: Ager CRISPR/Cas9 knockout


title: breast cancer_SM470

value: L


title: breast cancer_SM469

value: Cytology


title: lung alveolar organoid, Rbms3 knockout, plate1-4 well F03

description: Library name: 1-4_F03_RBMS3

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Rbms3 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate1-4 well F02

description: Library name: 1-4_F02_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM464


title: breast cancer_SM462


title: lung alveolar organoid, Manf knockout, plate1-4 well E11

description: Library name: 1-4_E11_MANF

value: Manf CRISPR/Cas9 knockout


title: lung alveolar organoid, Inhba knockout, plate1-4 well E10

description: Library name: 1-4_E10_INHBA

value: Inhba CRISPR/Cas9 knockout


title: lung alveolar organoid, Ulk1 knockout, plate1-4 well E09

description: Library name: 1-4_E09_ULK1

value: Ulk1 CRISPR/Cas9 knockout


title: breast cancer_SM460

value: P


title: breast cancer_SM457

value: III


title: breast cancer_SM458

value: I

value: Surgical Tissue Sample


title: breast cancer_SM449

value: N


title: lung alveolar organoid, Nkx21 knockout, plate1-4 well E06

description: Library name: 1-4_E06_NKX21

value: Nkx21 CRISPR/Cas9 knockout


title: breast cancer_SM445

value: Needle Biopsy Sample


title: lung alveolar organoid, Usp30 knockout, plate1-4 well E07

description: Library name: 1-4_E07_USP30

value: Usp30 CRISPR/Cas9 knockout


title: lung alveolar organoid, Nfe2l2 knockout, plate1-4 well E08

description: Library name: 1-4_E08_NFE2L2

value: Nfe2l2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Twist1 knockout, plate1-4 well E05

description: Library name: 1-4_E05_TWIST1

value: Twist1 CRISPR/Cas9 knockout


title: breast cancer_SM444

value: Tissue


title: lung alveolar organoid, Sox4 knockout, plate1-4 well E04

description: Library name: 1-4_E04_SOX4

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Sox4 CRISPR/Cas9 knockout


title: breast cancer_SM442

value: IIB

value: Cytology


title: lung alveolar organoid, Tigit knockout, plate1-4 well E03

description: Library name: 1-4_E03_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM439

value: IV


title: lung alveolar organoid, Tfcp2l1 knockout, plate1-4 well E02

description: Library name: 1-4_E02_TFCP2L1

value: Tfcp2l1 CRISPR/Cas9 knockout


title: breast cancer_SM438

value: P


title: lung alveolar organoid, Il1a knockout, plate1-4 well D11

description: Library name: 1-4_D11_IL1A

value: Il1a CRISPR/Cas9 knockout


title: breast cancer_SM435

value: IIA

value: Surgical Tissue Sample


title: lung alveolar organoid, Fgf7 knockout, plate1-4 well D10

description: Library name: 1-4_D10_FGF7

value: Fgf7 CRISPR/Cas9 knockout


title: breast cancer_SM434

value: N


title: breast cancer_SM429

value: L

value: III

value: Needle Biopsy Sample


title: lung alveolar organoid, Keap1 knockout, plate1-4 well D08

description: Library name: 1-4_D08_KEAP1

value: Keap1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tfeb knockout, plate1-4 well D09

description: Library name: 1-4_D09_TFEB

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Tfeb CRISPR/Cas9 knockout


title: breast cancer_SM428

value: Tissue


title: breast cancer_SM430


title: lung alveolar organoid, Tigit knockout, plate1-4 well D07

description: Library name: 1-4_D07_TIGIT


title: E9.5-scRNA-T37KO-SC-3

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

country: China

institute: Chinese Academy of Science

description: Library name: E9.5-scRNA-T37KO-SC-3

library_source: transcriptomic single cell

data_processing:
For scRNA-seq, quality control of the raw FASTQ data was conducted using Trim Galore (v0.6.4), followed by read alignment to the mm10 genome with STAR (v2.7.3a) under default settings. Only uniquely mapped reads were retained and filtered with Sambamba (v1.0.0). Mapping quality was assessed using RSeQC (v3.0.0). Raw counts were obtained with featureCounts (v2.0.6), while TPM and FPKM values were computed using StringTie (v2.0). For bulk RNA-seq, the raw RNA-seq data were first trimmed with TrimGalore (v0.6.10) to remove low-quality sequences and adapter contamination. Clean reads were then aligned to the mm10 reference genome using HISAT2 (v2.2.1). Gene-level counts were obtained with featureCounts (v2.0.1) based on UCSC GTF annotation, and FPKM values were calculated using Cufflinks (v2.2.1).
Assembly: mm10
Supplementary files format and content: Txt file includes raw counts for each smaple.

organism: Mus musculus

source_name: E9.5 embryo

extract_protocol:
For scRNA-seq, the E8.5 Nanog-EGFP transgenic embryos and E9.5 Oct4-EGFP transgenic embryos were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher, Cat#25200072) at 37 °C. After digestion, the embryos were gently pipetted and resuspended in the H-CZB medium. The single PGC from wild-type and Trim37ko embryos were picked by a Piezo-drill micromanipulator and transferred into a 200 µL tube containing 3.5 µL lysis buffer. For bulk RNA-seq, E9.25 control and Trim37ko embryos carrying Nanog-EGFP transgene were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher Scientific, Cat#25200072) at 37 °C. Following digestion, Nanog-EGFP positive PGCs were isolated from the suspension via FACS. Approximately 80 PGCs per sample were transferred into a 200 µL tube containing 3.5 µL of lysis buffer.
The lysate was then subjected to cDNA amplification using the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712).
Libraries of RNA-seq subjected to deep sequencing on Illumina NovaSeq6000 platform following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads by Genergy Biotechnology Co. Ltd. (Shanghai, China).

tag: tissue

value: E9.5 embryo

tag: strain

tag: genetic modification

value: Control

tag: time


title: lung alveolar organoid, Ttf1 knockout, plate1-4 well D06

description: Library name: 1-4_D06_TTF1

value: Ttf1 CRISPR/Cas9 knockout


title: breast cancer_SM425


title: lung alveolar organoid, Tns1 knockout, plate1-4 well D05

description: Library name: 1-4_D05_TNS1

value: Tns1 CRISPR/Cas9 knockout


title: breast cancer_SM424

value: P


title: lung alveolar organoid, Rnf43 knockout, plate1-4 well D04

description: Library name: 1-4_D04_RNF43

value: Rnf43 CRISPR/Cas9 knockout


title: breast cancer_SM423

value: IIA

value: Cytology


title: lung alveolar organoid, Npnt knockout, plate1-4 well D03

description: Library name: 1-4_D03_NPNT

value: Npnt CRISPR/Cas9 knockout


title: breast cancer_SM422

value: N

value: I

value: Surgical Tissue Sample


title: lung alveolar organoid, Ror1 knockout, plate1-4 well D02

description: Library name: 1-4_D02_ROR1

value: Ror1 CRISPR/Cas9 knockout


title: breast cancer_SM420

value: L


title: lung alveolar organoid, Pla2g15 knockout, plate1-4 well C11

description: Library name: 1-4_C11_PLA2G15

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Pla2g15 CRISPR/Cas9 knockout


title: lung alveolar organoid, Bmp10 knockout, plate1-4 well C10

description: Library name: 1-4_C10_BMP10

value: Bmp10 CRISPR/Cas9 knockout


title: breast cancer_SM418

value: Tissue


title: Pseudohyphal C. auris cells, untreated, repeated biological replicate 4

city: Szeged

first: Krisztián

last: Laczi

address: 52. Közép Fasor

department: Biotechnology and Microbiology

country: Hungary

institute: University of Szeged

description: Library name: CaurU4

data_processing:
Quality filtering was done with Trimmomatic 0.39
The quality filtered reads were mapped on the reference with STAR
Rsubread's featureCounts module was used to compute read numbers
Assembly: C. albicans: GCF_000182965.3, C. auris: GCF_003013715.1
Supplementary files format and content: tab delimited text format containing the read counts of the individual samples

organism: Candidozyma auris

source_name: Pseudohyphal

extract_protocol:
Early-stage filamentous C. albicans cells were thawed, refrozen in liquid nitrogen, and resuspended in lysis buffer in bashing lysis tubes, followed by mechanical disruption using a Tissuelyser LT (Qiagen) for 20 min at 50 Hz. C. auris pseudohyphae were ground for 1 min with nuclease-free sand using a microcentrifuge tube–compatible glass pestle, frozen again in liquid nitrogen, and reground in lysis buffer. Lysates were centrifuged (9,000 × g, 2 min), and total RNA was purified using the Quick-RNA Plant Miniprep Kit (Zymo Research, Tustin, CA, USA) according to the manufacturer’s instructions.
total RNA library preparation protocol for Illumina NovaSeq X Plus 2x150 nt: Novogene NGS library preparation kit

value: Pseudohyphal

tag: treatment

value: Untreated


title: Pseudohyphal C. auris cells, untreated, repeated biological replicate 3

description: Library name: CaurU3


title: lung alveolar organoid, Tigit knockout, plate1-4 well C09

description: Library name: 1-4_C09_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM417

value: P


title: Pseudohyphal C. auris cells, untreated, repeated biological replicate 2

description: Library name: CaurU2


title: Pseudohyphal C. auris cells, untreated, repeated biological replicate 1

description: Library name: CaurU1


title: breast cancer_SM419

value: Needle Biopsy Sample


title: lung alveolar organoid, Prkn knockout, plate1-4 well C08

description: Library name: 1-4_C08_PRKN

value: Prkn CRISPR/Cas9 knockout


title: breast cancer_SM416

value: IIA


title: Pseudohyphal C. auris cells, 25 µg mL−1 NFAP2 treated, biological replicate 4

description: Library name: CaurT4


title: Pseudohyphal C. auris cells, 25 µg mL−1 NFAP2 treated, biological replicate 3

description: Library name: CaurT3


title: lung alveolar organoid, Il1a knockout, plate1-4 well C07

description: Library name: 1-4_C07_IL1A

value: Il1a CRISPR/Cas9 knockout


title: breast cancer_SM414

value: N

value: III


title: Pseudohyphal C. auris cells, 25 µg mL−1 NFAP2 treated, biological replicate 1

description: Library name: CaurT1


title: Pseudohyphal C. auris cells, 25 µg mL−1 NFAP2 treated, biological replicate 2

description: Library name: CaurT2


title: lung alveolar organoid, Trp63 knockout, plate1-4 well C06

description: Library name: 1-4_C06_TRP63

value: Trp63 CRISPR/Cas9 knockout


title: breast cancer_SM412

value: IIB


title: Pseudohyphal C. auris cells, untreated, biological replicate 2

description: Library name: CaurU6


title: lung alveolar organoid, Sftpd knockout, plate1-4 well C05

description: Library name: 1-4_C05_SFTPD

value: Sftpd CRISPR/Cas9 knockout


title: Pseudohyphal C. auris cells, untreated, biological replicate 1

description: Library name: CaurU5


title: Pseudohyphal C. auris cells, 3.12 µg mL−1 NFAP2 treated, biological replicate 3

description: Library name: CaurT7


title: breast cancer_SM411


title: Pseudohyphal C. auris cells, 3.12 µg mL−1 NFAP2 treated, biological replicate 2

description: Library name: CaurT6


title: lung alveolar organoid, Mecom knockout, plate1-4 well C03

description: Library name: 1-4_C03_MECOM

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Mecom CRISPR/Cas9 knockout


title: Pseudohyphal C. auris cells, untreated, biological replicate 3

description: Library name: CaurU7


title: breast cancer_SM409

value: Surgical Tissue Sample


title: Pseudohyphal C. auris cells, 3.12 µg mL−1 NFAP2 treated, biological replicate 1

description: Library name: CaurT5


title: lung alveolar organoid, Tead1 knockout, plate1-4 well C02

description: Library name: 1-4_C02_TEAD1

value: Tead1 CRISPR/Cas9 knockout


title: sclera, pigmented hyperopic, replicate 4

city: Baton Rouge

first: Sujoy

last: Ghosh

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

data_processing:
The quality of RNA-seq reads was ascertained via FASTQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc)
Adapter trimming was performed via Trimmomatic v0.36 (https://www.usadellab.org/cms/?page=trimmomatic)
Sequencing reads were mapped to the Cavia porcellus reference genome (CavPor3.0) and annotation (Cavpor3.0.100) via STAR (2.7.5+)
Raw count matrices of RNA sequencing data were obtained via htseq-count v0.13.5 (https://htseq.readthedocs.io/en/master/index.html) and further processed for gene quantification and identification of differentially expressed genes using the limma package
Gene counts were log2 transformed and normalized for sequencing depth via the trimmed means of M values (TMM) method
Assembly: CavPor3.0 from ENSEMBL100
Supplementary files format and content: Each file contains unfiltered raw data (not normalized, not log transformed) for all genes

organism: Cavia porcellus

source_name: Sclera

growth_protocol: Animals were bred on site. Eighteen albino and nine pigmented guinea pigs (Elm Hill Labs, Chelmsford, MA, USA) were kept in a 12-hour/12-hour light/dark cycle with free access to water and food. Pups were housed with their parents in transparent plastic wire-top cages until postnatal day 14 (D14). All animal care and treatments in this study conformed to the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research. Experimental protocols were approved by the Institutional Animal Care and Use Committee of SingHealth (AAALAC Accredited; 2020/SHS/1567).

extract_protocol:
Total RNAs were extracted from each sample via TRIzol (Life Technologies)
Ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Following is the workflow of library construction:

treatment_protocol: Animals were followed-up for ocular traits and physiological refractive development, biometric data, including refraction and axial length, were collected at day 7 and day 14 longitudinally. All refractive errors came from spontaneously developed physiological refractive errors.

value: Sclera

value: Pigmented Hyperopic


title: lung alveolar organoid, Gdf2 knockout, plate1-4 well B11

description: Library name: 1-4_B11_GDF2

value: Gdf2 CRISPR/Cas9 knockout


title: retina, pigmented hyperopic, replicate 4

source_name: Retina

value: Retina


title: choroid, pigmented hyperopic, replicate 4

source_name: Choroid

value: Choroid


title: breast cancer_SM403

value: P

value: Tissue


title: breast cancer_SM405

value: L

value: IIA


title: sclera, pigmented hyperopic, replicate 3


title: lung alveolar organoid, Ccbe1 knockout, plate1-4 well B10

description: Library name: 1-4_B10_CCBE1

value: Ccbe1 CRISPR/Cas9 knockout


title: choroid, pigmented hyperopic, replicate 2


title: breast cancer_SM399

value: N

value: Needle Biopsy Sample


title: retina, pigmented hyperopic, replicate 3


title: breast cancer_SM401


title: choroid, pigmented hyperopic, replicate 3


title: sclera, pigmented hyperopic, replicate 1


title: lung alveolar organoid, Pink1 knockout, plate1-4 well B08

description: Library name: 1-4_B08_PINK1

value: Pink1 CRISPR/Cas9 knockout


title: breast cancer_SM400

value: IIB


title: lung alveolar organoid, Trp53 knockout, plate1-4 well B06

description: Library name: 1-4_B06_TRP53

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Trp53 CRISPR/Cas9 knockout


title: retina, pigmented hyperopic, replicate 1


title: retina, pigmented hyperopic, replicate 2


title: lung alveolar organoid, Acp6 knockout, plate1-4 well B07

description: Library name: 1-4_B07_ACP6

value: Acp6 CRISPR/Cas9 knockout


title: breast cancer_SM397

value: Surgical Tissue Sample


title: lung alveolar organoid, Tdtomato knockout, plate1-4 well B05

description: Library name: 1-4_B05_TDTOMATO

value: Tdtomato CRISPR/Cas9 knockout


title: choroid, pigmented hyperopic, replicate 1

value: Pigmented Hyperopic


title: sclera, pigmented hyperopic, replicate 2

value: Sclera


title: breast cancer_SM396


title: sclera, albino hyperopic, replicate 4

value: Albino Hyperopic


title: choroid, albino hyperopic, replicate 4

value: Retina


title: lung alveolar organoid, Tigit knockout, plate1-4 well B04

description: Library name: 1-4_B04_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: retina, albino hyperopic, replicate 4

value: Choroid


title: breast cancer_SM393

value: P

value: IIA

value: Tissue


title: sclera, albino hyperopic, replicate 3


title: lung alveolar organoid, Glis3 knockout, plate1-4 well B03

description: Library name: 1-4_B03_GLIS3

value: Glis3 CRISPR/Cas9 knockout


title: retina, albino hyperopic, replicate 3


title: breast cancer_SM392

value: N

value: III

value: Cytology

value: Needle Biopsy Sample


title: sclera, albino hyperopic, replicate 2


title: choroid, albino hyperopic, replicate 3


title: lung alveolar organoid, Met knockout, plate1-4 well B02

description: Library name: 1-4_B02_MET

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Met CRISPR/Cas9 knockout


title: retina, albino hyperopic, replicate 2


title: choroid, albino hyperopic, replicate 2


title: breast cancer_SM388

value: I

value: Surgical Tissue Sample


title: breast cancer_SM391

value: IIB


title: lung alveolar organoid, Tigit knockout, plate1-3 well G11

description: Library name: 1-3_G11_TIGIT


title: sclera, albino myopic, replicate 4

value: Sclera

value: Albino Myopic


title: lung alveolar organoid, Tdtomato knockout, plate1-3 well G10

description: Library name: 1-3_G10_TDTOMATO

value: Tdtomato CRISPR/Cas9 knockout


title: breast cancer_SM387


title: choroid, albino myopic, replicate 4

value: Choroid


title: retina, albino myopic, replicate 4

value: Retina


title: lung alveolar organoid, Becn1 knockout, plate1-3 well G09

description: Library name: 1-3_G09_BECLN1

value: Becn1 CRISPR/Cas9 knockout


title: sclera, albino myopic, replicate 3


title: breast cancer_SM383

value: P

value: Tissue


title: retina, albino myopic, replicate 3


title: lung alveolar organoid, Ern1 knockout, plate1-3 well G08

description: Library name: 1-3_G08_ERN1

value: Ern1 CRISPR/Cas9 knockout


title: breast cancer_SM382

value: N

value: III


title: choroid, albino myopic, replicate 3


title: sclera, albino myopic, replicate 2


title: breast cancer_SM381

value: Cytology


title: retina, albino myopic, replicate 2


title: lung alveolar organoid, Nr1d2 knockout, plate1-3 well G07

description: Library name: 1-3_G07_NR1D2

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Nr1d2 CRISPR/Cas9 knockout


title: lung alveolar organoid, Hhip knockout, plate1-3 well G06

description: Library name: 1-3_G06_HHIP

value: Hhip CRISPR/Cas9 knockout


title: retina, albino myopic, replicate 1


title: breast cancer_SM379

value: IIA

value: Surgical Tissue Sample


title: choroid, albino myopic, replicate 2


title: lung alveolar organoid, Chrm3 knockout, plate1-3 well G05

description: Library name: 1-3_G05_CHRM3

value: Chrm3 CRISPR/Cas9 knockout


title: sclera, albino myopic, replicate 1

value: Sclera

value: Albino Myopic


title: breast cancer_SM377

value: IIB

value: Needle Biopsy Sample


title: choroid, albino myopic, replicate 1

value: Choroid


title: sclera, albino hyperopic, replicate 1

value: Albino Hyperopic


title: breast cancer_SM374

value: P

value: IV


title: retina, albino hyperopic, replicate 1

value: Retina


title: lung alveolar organoid, Cacna2d3 knockout, plate1-3 well G04

description: Library name: 1-3_G04_CACNA2D3

value: Cacna2d3 CRISPR/Cas9 knockout


title: choroid, albino hyperopic, replicate 1


title: lung alveolar organoid, Serpina1a knockout, plate1-3 well G03

description: Library name: 1-3_G03_SERPINA1A

value: Serpina1a CRISPR/Cas9 knockout


title: breast cancer_SM373

value: N

value: Tissue


title: Smad4KO_ChIP-seq_H3K27ac_rep2

city: Nanjing

first: Lei

last: Chen

address: No.2 Sipailou

institute: Southeast University

description:
Library name: Smad4KO_ChIP-seq_H3K27ac_rep2
Merged2_Smad4KO_ChIP-seq_macs2_q001.bed

library_source: genomic

data_processing:
For ChIP-seq, raw sequencing reads (FASTQ format) underwent quality control using FastQC (v0.12.1). Reads were then aligned to mouse (mm9) reference genome using Bowtie2 (v2.5.1) with default parameters, generating BAM format alignment files. BigWig coverage files were created from BAM files via deepTools48 (v3.5.4) bamCoverage with RPKM normalization, read extension to fragment length, and exclusion of duplicate reads. Genomic interval operations (merge/intersect/subtract) were performed using BEDTools (v2.31.1). Chromatin state dynamics were profiled with Haystack (v0.5.5) using quantile-normalized BigWigs. Peak calling was executed with MACS2 (v2.2.6) to generate BED-format peak files. Finally, normalized BigWig tracks were visualized in the Integrative Genomics Viewer (IGV v2.17.1).
Assembly: ChIP-seq: mm9
Supplementary files format and content: ChIP-seq: bigwig, Peaks BED files

molecule: genomic DNA

source_name: Smad4KO duodenal epithelium

extract_protocol: The duodenum was flushed with cold PBS, opened longitudinally, and cut into pieces. Epithelium was released by incubation in 3 mM EDTA/PBS at 4°C with rotation and shaking; the supernatant was collected after discarding the tissue. For MNase-ChIP, isolated epithelial cells were resuspended in digestion buffer (50 mM Tris-HCl pH 7.6, 1 mM CaCl₂, 0.2% Triton X-100, 5 mM Na butyrate, protease inhibitor cocktails) and digested with 0.67 U/ml MNase (Sigma #N3755) for 5 min at 37°C. The reaction was stopped with 5 mM EDTA/10 mM Tris (pH 7.6), and samples were dialyzed into chromatin RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 1% Triton X-100). Immunoprecipitation was performed overnight at 4°C using an H3K27ac antibody (Abcam ab4729). Further processing of the IP material followed the standard sonication-ChIP protocol (final SDS concentration of 0.13%). Libraries were prepared with the Rubicon Genomics ThruPLEX DNA-seq Kit.

value: Smad4KO duodenal epithelium

value: Villin-CreERT2; Smad4f/f

value: tamoxifen 50mg/kg/day


title: lung alveolar organoid, Pid1 knockout, plate1-3 well G02

description: Library name: 1-3_G02_PID1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Pid1 CRISPR/Cas9 knockout


title: Smad4KO_ChIP-seq_H3K27ac_rep1

description:
Library name: Smad4KO_ChIP-seq_H3K27ac_rep1
Merged2_Smad4KO_ChIP-seq_macs2_q001.bed


title: WT_ChIP-seq_H3K27ac

description: Library name: WT_ChIP-seq_H3K27ac

source_name: WT duodenal epithelium

extract_protocol: The duodenum was flushed with cold PBS, opened longitudinally, and cut into pieces. Epithelium was released by incubation in 3 mM EDTA/PBS at 4°C with rotation and shaking; the supernatant was collected after discarding the tissue. For MNase-ChIP, isolated epithelial cells were resuspended in digestion buffer (50 mM Tris-HCl pH 7.6, 1 mM CaCl₂, 0.2% Triton X-100, 5 mM Na butyrate, plus protease inhibitors) and digested with 0.67 U/ml MNase (Sigma #N3755) for 5 min at 37°C. The reaction was stopped with 5 mM EDTA/10 mM Tris (pH 7.6), and samples were dialyzed into chromatin RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 1% Triton X-100). Immunoprecipitation was performed overnight at 4°C using an H3K27Ac antibody (Abcam ab4729). Further processing of the IP material followed the standard sonication-ChIP protocol (final SDS concentration of 0.13%). Libraries were prepared with the Rubicon Genomics ThruPLEX DNA-seq Kit.

value: WT duodenal epithelium

value: WT

value: oil vehicle


title: breast cancer_SM372

value: IIB

value: Needle Biopsy Sample


title: WT-hpca1-WT_EL_Systemic3_rep3

city: Columbia

first: Sameep

last: Dhakal

state: MO

address: 1201 Rollins St.

department: Institute for data science and Informatics

institute: University of Missouri

description:
Library name: WhW_S3_EL_3
Chain of WT–hpcal1–WT plants, systemic leaf 3, elevated light, replicate 3

data_processing:
Read quality control was performed using Trim Galore v0.6.10 and FastQC v0.12.1. Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence. Subsequently, the processed reads were mapped to the Gmax_880_v6.0 whole genome using Hisat2 v2.2.1. Samtools v1.18 was used to sort the bam files which were subjected toranscript assembly and quantification using Cufflinks v2.2.1. Differential expression analysis was performed later using Cuffdiff v2.2.1, comparing control conditions with different stress and .
Assembly: Arabidopsis_thaliana TAIR10
Supplementary files format and content: processed data files are in format txt and it contains the gene names along with the fpkm values for each of the replicates.

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Seeds were germinated and grown on peat pellets (Jiffy-7; Jiffy International, Kristiansand, Norway), under controlled conditions of 50 µmol photons s−1 m−2, 10-h/14-h light/dark cycle at 22 °C/20 °C day/night and 400 μmol mol−1 CO2 for 4 to 5 weeks. Plants were then distributed in different treatment groups.

extract_protocol:
For each biological repeat, leaves were pooled together from 10-15 different plants and flash frozen in liquid nitrogen. RNA from samples was isolated using RNeasy plant mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: Individual plants were positioned so that they did not touch any other plant. For the chain and community plant setups, where leaf-to-leaf contact was required, a solution containing 0.05 M phosphate buffer (pH 7.4), 0.01% (v/v) Silwet L-77, and 0.05% agarose was applied to ensure contact between leaves.

value: Leaves

value: WT (Col-0)

value: Chain of WT–hpcal1–WT plants, systemic 3 leaf elevated light 30 min


title: breast cancer_SM371

value: P

value: IIA

value: Surgical Tissue Sample


title: WT-hpca1-WT_EL_Systemic3_rep1

description:
Library name: WhW_S3_EL_1
Chain of WT–hpcal1–WT plants, systemic leaf 3, elevated light, replicate 1


title: WT-hpca1-WT_EL_Systemic3_rep2

description:
Library name: WhW_S3_EL_2
Chain of WT–hpcal1–WT plants, systemic leaf 3, elevated light, replicate 2


title: lung alveolar organoid, Rad21 knockout, plate1-3 well F11

description: Library name: 1-3_F11_RAD21

value: Rad21 CRISPR/Cas9 knockout


title: breast cancer_SM369

value: N

value: I

value: Tissue


title: lung alveolar organoid, Atg16l1 knockout, plate1-3 well F09

description: Library name: 1-3_F09_ATG16L1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Atg16l1 CRISPR/Cas9 knockout


title: WT-hpca1-WT_CT_Systemic3_rep3

description:
Library name: WhW_S3_CT_3
Chain of WT–hpcal1–WT plants, systemic leaf 3, control, replicate 3

value: Chain of WT–hpcal1–WT plants, systemic 3 leaf no stress


title: WT-hpca1-WT_CT_Systemic3_rep2

description:
Library name: WhW_S3_CT_2
Chain of WT–hpcal1–WT plants, systemic leaf 3, control, replicate 2


title: WT-hpca1-WT_CT_Systemic3_rep1

description:
Library name: WhW_S3_CT_1
Chain of WT–hpcal1–WT plants, systemic leaf 3, control, replicate 1


title: lung alveolar organoid, Xbp1 knockout, plate1-3 well F10

description: Library name: 1-3_F10_XBP1

value: Xbp1 CRISPR/Cas9 knockout


title: WT-hpca1-WT_EL_Systemic2_rep3

description:
Library name: WhW_S2_EL_3
Chain of WT–hpcal1–WT plants, systemic leaf 2, elevated light, replicate 3

value: Chain of WT–hpcal1–WT plants, systemic 2 leaf elevated light 30 min


title: breast cancer_SM365


title: WT-hpca1-WT_EL_Systemic2_rep2

description:
Library name: WhW_S2_EL_2
Chain of WT–hpcal1–WT plants, systemic leaf 2, elevated light, replicate 2


title: WT-hpca1-WT_EL_Systemic2_rep1

description:
Library name: WhW_S2_EL_1
Chain of WT–hpcal1–WT plants, systemic leaf 2, elevated light, replicate 1


title: breast cancer_SM364

value: L

value: IIB


title: WT-hpca1-WT_CT_Systemic2_rep3

description:
Library name: WhW_S2_CT_3
Chain of WT–hpcal1–WT plants, systemic leaf 2, control, replicate 3

value: Leaves

value: Chain of WT–hpcal1–WT plants, systemic 2 leaf no stress


title: lung alveolar organoid, Nr1d1 knockout, plate1-3 well F07

description: Library name: 1-3_F07_NR1D1

value: Nr1d1 CRISPR/Cas9 knockout


title: breast cancer_SM368

value: P


title: lung alveolar organoid, Eif2b1 knockout, plate1-3 well F08

description: Library name: 1-3_F08_EIF2B1

value: Eif2b1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Fam13a knockout, plate1-3 well F06

description: Library name: 1-3_F06_FAM13A

value: Fam13a CRISPR/Cas9 knockout


title: WT-hpca1-WT_CT_Systemic2_rep2

description:
Library name: WhW_S2_CT_2
Chain of WT–hpcal1–WT plants, systemic leaf 2, control, replicate 2


title: breast cancer_SM362

value: III

value: Needle Biopsy Sample


title: WT-hpca1-WT_CT_Systemic2_rep1

description:
Library name: WhW_S2_CT_1
Chain of WT–hpcal1–WT plants, systemic leaf 2, control, replicate 1


title: WT-hpca1-WT_EL_Systemic1_rep3

description:
Library name: WhW_S1_EL_3
Chain of WT–hpcal1–WT plants, systemic leaf 1, elevated light, replicate 3

value: WT (Col-0)

value: Chain of WT–hpcal1–WT plants, systemic 1 leaf elevated light 30 min


title: WT-hpca1-WT_EL_Systemic1_rep2

description:
Library name: WhW_S1_EL_2
Chain of WT–hpcal1–WT plants, systemic leaf 1, elevated light, replicate 2


title: lung alveolar organoid, Terf1 knockout, plate1-3 well F05

description: Library name: 1-3_F05_TERF1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Terf1 CRISPR/Cas9 knockout


title: breast cancer_SM360

value: N

value: I

value: Tissue

value: Surgical Tissue Sample


title: WT-hpca1-WT_EL_Systemic1_rep1

description:
Library name: WhW_S1_EL_1
Chain of WT–hpcal1–WT plants, systemic leaf 1, elevated light, replicate 1


title: WT-hpca1-WT_CT_Systemic1_rep2

description:
Library name: WhW_S1_CT_2
Chain of WT–hpcal1–WT plants, systemic leaf 1, control, replicate 2

value: Chain of WT–hpcal1–WT plants, systemic 1 leaf no stress


title: lung alveolar organoid, Rbms3 knockout, plate1-3 well F03

description: Library name: 1-3_F03_RBMS3

value: Rbms3 CRISPR/Cas9 knockout


title: WT-hpca1-WT_CT_Systemic1_rep1

description:
Library name: WhW_S1_CT_1
Chain of WT–hpcal1–WT plants, systemic leaf 1, control, replicate 1

value: Leaves


title: WT-hpca1-WT_EL_Local_rep3

description:
Library name: WhW_L_EL_3
Chain of WT–hpcal1–WT plants, local leaf, elevated light, replicate 3

value: Chain of WT–hpcal1–WT plants, local leaf elevated light 30 min


title: breast cancer_SM358

value: P

value: IIB


title: lung alveolar organoid, Tigit knockout, plate1-3 well F02

description: Library name: 1-3_F02_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: lung alveolar organoid, Ager knockout, plate1-3 well F04

description: Library name: 1-3_F04_AGER

value: Ager CRISPR/Cas9 knockout


title: breast cancer_SM357

value: IIA


title: lung alveolar organoid, Manf knockout, plate1-3 well E11

description: Library name: 1-3_E11_MANF

value: Manf CRISPR/Cas9 knockout


title: breast cancer_SM356


title: WT-hpca1-WT_CT_Systemic1_rep3

description:
Library name: WhW_S1_CT_3
Chain of WT–hpcal1–WT plants, systemic leaf 1, control, replicate 3

value: WT (Col-0)


title: breast cancer_SM355


title: WT-hpca1-WT_CT_Local_rep3

description:
Library name: WhW_L_CT_3
Chain of WT–hpcal1–WT plants, local leaf, control, replicate 3

value: Chain of WT–hpcal1–WT plants, local leaf no stress


title: WT-hpca1-WT_EL_Local_rep1

description:
Library name: WhW_L_EL_1
Chain of WT–hpcal1–WT plants, local leaf, elevated light, replicate 1


title: WT-hpca1-WT_CT_Local_rep2

description:
Library name: WhW_L_CT_2
Chain of WT–hpcal1–WT plants, local leaf, control, replicate 2


title: WT-hpca1-WT_EL_Local_rep2

description:
Library name: WhW_L_EL_2
Chain of WT–hpcal1–WT plants, local leaf, elevated light, replicate 2


title: lung alveolar organoid, Inhba knockout, plate1-3 well E10

description: Library name: 1-3_E10_INHBA

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Inhba CRISPR/Cas9 knockout


title: breast cancer_SM354

value: N

value: Needle Biopsy Sample


title: lung alveolar organoid, Ulk1 knockout, plate1-3 well E09

description: Library name: 1-3_E09_ULK1

value: Ulk1 CRISPR/Cas9 knockout


title: 3WT_EL_Systemic3_rep2

description:
Library name: WT_S3_EL_2
Chain of 3 wild-type plants, systemic leaf 3, elevated light, replicate 2

value: Chain of 3 wild-type plants, systemic 3 leaf elevated light 30 min


title: breast cancer_SM352

value: Tissue

value: Surgical Tissue Sample


title: WT-hpca1-WT_CT_Local_rep1

description:
Library name: WhW_L_CT_1
Chain of WT–hpcal1–WT plants, local leaf, control, replicate 1

value: Leaves


title: lung alveolar organoid, Usp30 knockout, plate1-3 well E07

description: Library name: 1-3_E07_USP30

value: Usp30 CRISPR/Cas9 knockout


title: 3WT_EL_Systemic3_rep3

description:
Library name: WT_S3_EL_3
Chain of 3 wild-type plants, systemic leaf 3, elevated light, replicate 3


title: 3WT_EL_Systemic3_rep1

description:
Library name: WT_S3_EL_1
Chain of 3 wild-type plants, systemic leaf 3, elevated light, replicate 1


title: 3WT_CT_Systemic3_rep2

description:
Library name: WT_S3_CT_2
Chain of 3 wild-type plants, systemic leaf 3, control, replicate 2

value: Chain of 3 wild-type plants, systemic 3 leaf no stress


title: lung alveolar organoid, Nkx21 knockout, plate1-3 well E06

description: Library name: 1-3_E06_NKX21

value: Nkx21 CRISPR/Cas9 knockout


title: 3WT_CT_Systemic3_rep1

description:
Library name: WT_S3_CT_1
Chain of 3 wild-type plants, systemic leaf 3, control, replicate 1


title: breast cancer_SM351

value: P

value: I


title: breast cancer_SM350

value: IIB


title: 3WT_CT_Systemic3_rep3

description:
Library name: WT_S3_CT_3
Chain of 3 wild-type plants, systemic leaf 3, control, replicate 3

value: WT (Col-0)


title: lung alveolar organoid, Twist1 knockout, plate1-3 well E05

description: Library name: 1-3_E05_TWIST1

value: Twist1 CRISPR/Cas9 knockout


title: 3WT_EL_Systemic2_rep2

description:
Library name: WT_S2_EL_2
Chain of 3 wild-type plants, systemic leaf 2, elevated light, replicate 2

value: Chain of 3 wild-type plants, systemic 2 leaf elevated light 30 min


title: 3WT_EL_Systemic2_rep3

description:
Library name: WT_S2_EL_3
Chain of 3 wild-type plants, systemic leaf 2, elevated light, replicate 3


title: breast cancer_SM349


title: lung alveolar organoid, Sox4 knockout, plate1-3 well E04

description: Library name: 1-3_E04_SOX4

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Sox4 CRISPR/Cas9 knockout


title: breast cancer_SM348

value: N

value: III

value: Needle Biopsy Sample


title: 3WT_CT_Systemic2_rep2

description:
Library name: WT_S2_CT_2
Chain of 3 wild-type plants, systemic leaf 2, control, replicate 2

value: Chain of 3 wild-type plants, systemic 2 leaf no stress


title: 3WT_EL_Systemic2_rep1

description:
Library name: WT_S2_EL_1
Chain of 3 wild-type plants, systemic leaf 2, elevated light, replicate 1


title: 3WT_CT_Systemic2_rep3

description:
Library name: WT_S2_CT_3
Chain of 3 wild-type plants, systemic leaf 2, control, replicate 3


title: breast cancer_SM346

value: IIA

value: Tissue

value: Surgical Tissue Sample


title: breast cancer_SM347


title: lung alveolar organoid, Tfcp2l1 knockout, plate1-3 well E02

description: Library name: 1-3_E02_TFCP2L1

value: Tfcp2l1 CRISPR/Cas9 knockout


title: 3WT_EL_Systemic1_rep2

description:
Library name: WT_S1_EL_2
Chain of 3 wild-type plants, systemic leaf 1, elevated light, replicate 2

value: Leaves

value: Chain of 3 wild-type plants, systemic 1 leaf elevated light 30 min


title: 3WT_EL_Systemic1_rep1

description:
Library name: WT_S1_EL_1
Chain of 3 wild-type plants, systemic leaf 1, elevated light, replicate 1


title: 3WT_EL_Systemic1_rep3

description:
Library name: WT_S1_EL_3
Chain of 3 wild-type plants, systemic leaf 1, elevated light, replicate 3


title: lung alveolar organoid, Il1a knockout, plate1-3 well D11

description: Library name: 1-3_D11_IL1A

value: Il1a CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate1-3 well E03

description: Library name: 1-3_E03_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: 3WT_CT_Systemic1_rep3

description:
Library name: WT_S1_CT_3
Chain of 3 wild-type plants, systemic leaf 1, control, replicate 3

value: WT (Col-0)

value: Chain of 3 wild-type plants, systemic 1 leaf no stress


title: 3WT_CT_Systemic1_rep2

description:
Library name: WT_S1_CT_2
Chain of 3 wild-type plants, systemic leaf 1, control, replicate 2


title: 3WT_CT_Systemic2_rep1

description:
Library name: WT_S2_CT_1
Chain of 3 wild-type plants, systemic leaf 2, control, replicate 1


title: breast cancer_SM344

value: P


title: 3WT_CT_Systemic1_rep1

description:
Library name: WT_S1_CT_1
Chain of 3 wild-type plants, systemic leaf 1, control, replicate 1


title: breast cancer_SM343

value: Cytology


title: lung alveolar organoid, Fgf7 knockout, plate1-3 well D10

description: Library name: 1-3_D10_FGF7

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Fgf7 CRISPR/Cas9 knockout


title: 3WT_EL_Local_rep3

description:
Library name: WT_L_EL_3
Chain of 3 wild-type plants, local leaf, elevated light, replicate 3

value: Chain of 3 wild-type plants, local leaf elevated light 30 min


title: 3WT_EL_Local_rep2

description:
Library name: WT_L_EL_2
Chain of 3 wild-type plants, local leaf, elevated light, replicate 2


title: breast cancer_SM342

value: L

value: N


title: lung alveolar organoid, Tfeb knockout, plate1-3 well D09

description: Library name: 1-3_D09_TFEB

value: Tfeb CRISPR/Cas9 knockout


title: breast cancer_SM341

value: I

value: Tissue


title: 3WT_CT_Local_rep3

description:
Library name: WT_L_CT_3
Chain of 3 wild-type plants, local leaf, control, replicate 3

value: Chain of 3 wild-type plants, local leaf no stress


title: lung alveolar organoid, Tigit knockout, plate1-3 well D07

description: Library name: 1-3_D07_TIGIT


title: 3WT_EL_Local_rep1

description:
Library name: WT_L_EL_1
Chain of 3 wild-type plants, local leaf, elevated light, replicate 1

value: Leaves


title: breast cancer_SM340

value: Surgical Tissue Sample


title: 3WT_CT_Local_rep1

description:
Library name: WT_L_CT_1
Chain of 3 wild-type plants, local leaf, control, replicate 1


title: lung alveolar organoid, Ttf1 knockout, plate1-3 well D06

description: Library name: 1-3_D06_TTF1

value: Ttf1 CRISPR/Cas9 knockout


title: Community_Plant_Touching_for_one_week_Rep3

description:
Library name: Touch1w_3
Plant in community, touching other plants for one week, replicate 3

value: Community 1 week, no stress


title: 3WT_CT_Local_rep2

description:
Library name: WT_L_CT_2
Chain of 3 wild-type plants, local leaf, control, replicate 2

value: WT (Col-0)


title: breast cancer_ANON 12X

value: IIB


title: breast cancer_ANON 12Z

value: P

value: IIA


title: Community_Plant_Touching_for_one_week_Rep2

description:
Library name: Touch1w_2
Plant in community, touching other plants for one week, replicate 2


title: Community_Plant_Touching_for_one_hour_Rep3

description:
Library name: Touch1h_3
Plant in community, touching other plants for one hour, replicate 3

value: Community 1 hour, no stress


title: breast cancer_SM339


title: lung alveolar organoid, Tns1 knockout, plate1-3 well D05

description: Library name: 1-3_D05_TNS1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Tns1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Rnf43 knockout, plate1-3 well D04

description: Library name: 1-3_D04_RNF43

value: Rnf43 CRISPR/Cas9 knockout


title: Community_Plant_Touching_for_one_week_Rep1

description:
Library name: Touch1w_1
Plant in community, touching other plants for one week, replicate 1