Sample Set Annotation Tool: CD4+ TIL in human breast cancer

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

CD4+ T cells are critical regulators of immune responses, but their functional role in human breast cancer is relatively unknown. The goal of this study was to produce an image of CD4? T cells infiltrating breast tumors using limited ex vivo manipulation to better understand the in vivo differences associated with patient prognosis.

Hypothesis

Experimental Design

Experimental Variables

Controls

Methods

Additional Information

SuperSeries containing data from:

GSE36765 - Gene expression profiling of CD4+ T cells infiltrating human breast cancer (Discovery Set)

GSE36766 - Effect of human breast tumor supernatant on normal CD4+ T cells (Confirmation Set SN)

GSE36767 - Gene changes of CD4+ T cells infiltrating human breast cancer in the absence of tumor environment (Confirmation Set 24h)

Expected Samples:

60 Samples Loaded: 60

Species

Human (Homo sapiens)

Sample Source

Disease

Mixed Breast Cancer Types

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample_title	cell type	disease state	source tissue
GSM900526	PB Donor 1	purified CD4+ T cells	healthy	peripheral blood
GSM900527	PB Donor 2	purified CD4+ T cells	healthy	peripheral blood
GSM900528	PB Donor 3	purified CD4+ T cells	healthy	peripheral blood
GSM900529	PB Donor 4	purified CD4+ T cells	healthy	peripheral blood
GSM900530	PB Patient 1	purified CD4+ T cells	breast cancer	peripheral blood

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Sample ID	!Sample Title	Cell type	Treatment	Disease state	Source tissue
GSM900526	PB Donor 1	purified CD4+ T cells		healthy	peripheral blood
GSM900527	PB Donor 2	purified CD4+ T cells		healthy	peripheral blood
GSM900528	PB Donor 3	purified CD4+ T cells		healthy	peripheral blood
GSM900529	PB Donor 4	purified CD4+ T cells		healthy	peripheral blood
GSM900530	PB Patient 1	purified CD4+ T cells		breast cancer	peripheral blood
GSM900531	PB Patient 2	purified CD4+ T cells		breast cancer	peripheral blood
GSM900532	PB Patient 3	purified CD4+ T cells		breast cancer	peripheral blood
GSM900533	PB Patient 4	purified CD4+ T cells		breast cancer	peripheral blood
GSM900534	PB Patient 5	purified CD4+ T cells		breast cancer	peripheral blood
GSM900535	PB Patient 6	purified CD4+ T cells		breast cancer	peripheral blood
GSM900536	PB Patient 7	purified CD4+ T cells		breast cancer	peripheral blood
GSM900537	PB Patient 8	purified CD4+ T cells		breast cancer	peripheral blood
GSM900538	PB Patient 9	purified CD4+ T cells		breast cancer	peripheral blood
GSM900539	PB Patient 10	purified CD4+ T cells		breast cancer	peripheral blood
GSM900540	LN Patient 1	purified CD4+ T cells		breast cancer	lymph node
GSM900541	LN Patient 2	purified CD4+ T cells		breast cancer	lymph node
GSM900542	LN Patient 3	purified CD4+ T cells		breast cancer	lymph node
GSM900543	LN Patient 4	purified CD4+ T cells		breast cancer	lymph node
GSM900544	LN Patient 5	purified CD4+ T cells		breast cancer	lymph node
GSM900545	LN Patient 6	purified CD4+ T cells		breast cancer	lymph node
GSM900546	LN Patient 7	purified CD4+ T cells		breast cancer	lymph node
GSM900547	LN Patient 8	purified CD4+ T cells		breast cancer	lymph node
GSM900548	LN Patient 9	purified CD4+ T cells		breast cancer	lymph node
GSM900549	LN Patient 10	purified CD4+ T cells		breast cancer	lymph node
GSM900550	TIL Patient 1	purified CD4+ T cells		breast cancer	breast tumor
GSM900551	TIL Patient 2	purified CD4+ T cells		breast cancer	breast tumor
GSM900552	TIL Patient 3	purified CD4+ T cells		breast cancer	breast tumor
GSM900553	TIL Patient 4	purified CD4+ T cells		breast cancer	breast tumor
GSM900554	TIL Patient 5	purified CD4+ T cells		breast cancer	breast tumor
GSM900555	TIL Patient 6	purified CD4+ T cells		breast cancer	breast tumor
GSM900556	TIL Patient 7	purified CD4+ T cells		breast cancer	breast tumor
GSM900557	TIL Patient 8	purified CD4+ T cells		breast cancer	breast tumor
GSM900558	TIL Patient 9	purified CD4+ T cells		breast cancer	breast tumor
GSM900559	TIL Patient 10	purified CD4+ T cells		breast cancer	breast tumor
GSM900560	Memory CD4 NS at 24h, biological rep1	purified CD45RA-CD4+ T cells	untreated	healthy	peripheral blood
GSM900561	Memory CD4 NS at 24h, biological rep2	purified CD45RA-CD4+ T cells	untreated	healthy	peripheral blood
GSM900562	Memory CD4 NS at 24h, biological rep3	purified CD45RA-CD4+ T cells	untreated	healthy	peripheral blood
GSM900563	Memory CD4 NS + SN034 at 24h	purified CD45RA-CD4+ T cells	+ 24h treatment with SN from breast cancer patient 034	healthy	peripheral blood
GSM900564	Memory CD4 NS + SN043 at 24h	purified CD45RA-CD4+ T cells	+ 24h treatment with SN from breast cancer patient 043	healthy	peripheral blood
GSM900565	Memory CD4 NS + SN019 at 24h	purified CD45RA-CD4+ T cells	+ 24h treatment with SN from breast cancer patient 019	healthy	peripheral blood
GSM900566	Memory CD4 NS + SN027 at 24h	purified CD45RA-CD4+ T cells	+ 24h treatment with SN from breast cancer patient 027	healthy	peripheral blood
GSM900567	Memory CD4 S at 24h, biological rep1	purified CD45RA-CD4+ T cells	+ 24h stimulation	healthy	peripheral blood
GSM900568	Memory CD4 S at 24h, biological rep2	purified CD45RA-CD4+ T cells	+ 24h stimulation	healthy	peripheral blood
GSM900569	Memory CD4 S at 24h, biological rep3	purified CD45RA-CD4+ T cells	+ 24h stimulation	healthy	peripheral blood
GSM900570	Memory CD4 S + SN034 at 24h	purified CD45RA-CD4+ T cells	+ 24h stimulatin (anti-CD3 + anti-CD28) & treatment with SN from breast cancer patient 034	healthy	peripheral blood
GSM900571	Memory CD4 S + SN043 at 24h	purified CD45RA-CD4+ T cells	+ 24h stimulatin (anti-CD3 + anti-CD28) & treatment with SN from breast cancer patient 043	healthy	peripheral blood
GSM900572	Memory CD4 S + SN019 at 24h	purified CD45RA-CD4+ T cells	+ 24h stimulatin (anti-CD3 + anti-CD28) & treatment with SN from breast cancer patient 019	healthy	peripheral blood
GSM900573	Memory CD4 S + SN027 at 24h	purified CD45RA-CD4+ T cells	+ 24h stimulatin (anti-CD3 + anti-CD28) & treatment with SN from breast cancer patient 027	healthy	peripheral blood
GSM900574	TIL062 at T0	purified CD4+ T cells	none	breast cancer	breast tumor
GSM900575	TIL062 at 24h	purified CD4+ T cells	24 h incubation in X-VIVO 20	breast cancer	breast tumor
GSM900576	TIL064 at T0	purified CD4+ T cells	none	breast cancer	breast tumor
GSM900577	TIL064 at 24h	purified CD4+ T cells	24 h incubation in X-VIVO 20	breast cancer	breast tumor
GSM900578	RO at T0	purified CD45RA-CD4+ T cells	none	healthy	peripheral blood
GSM900579	RO at 24h	purified CD45RA-CD4+ T cells	24 h incubation in X-VIVO 20	healthy	peripheral blood
GSM900580	Total CD4 NS at 24h, biological rep1	CD4	none	healthy	peripheral blood
GSM900581	Total CD4 NS at 24h, biological rep2	CD4	none	healthy	peripheral blood
GSM900582	Total CD4 NS at 24h, biological rep3	CD4	none	healthy	peripheral blood
GSM900583	Total CD4 NS + SN014 at 24h	CD4	+ 24h treatment with SN from breast cancer patient 014	healthy	peripheral blood
GSM900584	Total CD4 NS + SN016 at 24h	CD4	+ 24h treatment with SN from breast cancer patient 016	healthy	peripheral blood
GSM900585	Total CD4 NS + SN034 at 24h	CD4	+ 24h treatment with SN from breast cancer patient 034	healthy	peripheral blood

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SIDRA